13-20189605-T-G

Variant names:

• chr13-20189605-T-G
• rs201895089
• NM_004004.6:c.-22-2A>C

Variant summary

Our verdict is Likely pathogenic. The variant received 0 ACMG points: 4P and 4B. BS1 PS3_Supporting PP1 PM3

This summary comes from the ClinGen Evidence Repository: The filtering allele frequency of the c.-22-2A>C variant in the GJB2 gene is 0.35% for Ashkenazi Jewish chromosomes in gnomAD v2.1.1 (95% CI of 47/10344), which meets the allele frequency threshold defined by the ClinGen Hearing Loss Expert Panel for considering strong evidence against pathogenicity for autosomal recessive hearing loss variants (BS1). However, based on the evidence outlined below, the ClinGen Hearing Loss Expert Panel believes that the evidence for the pathogenicity of this variant for nonsyndromic hearing loss outweighs its high allele frequency in population databases. Therefore, the BS1 code will not contribute to the overall classification. The c.-22-2A>C variant in the GJB2 gene has been detected in at least 9 patients with hearing loss in trans with the pathogenic c.35delG variant (PM3_Very Strong; PMID:25401782, 24039984, 33096615; Invitae internal data, SCV000935680.2; Children’s Hospital of Philadelphia internal data, Molecular Otolaryngology and Renal Research Laboratories internal data) and one individual with the the p.Leu90Pro variant suspected in trans (PMID:19814620). Phase was confirmed in at least 6 of these 10 observations.This variant has been reported to segregate with hearing loss in at least 2 family members (PP1; PMID:24039984). It was also identified in the heterozygous state without a second variant in 8 individuals with hearing loss, and in the biallelic state (with c.35delG) in one individual with reportedly normal hearing (GeneDx, ARUP internal data, SCV000680741.2, SCV000603828.1). Of note, the severity of hearing loss is reported to be mild-moderate in affected probands, some with onset in the third to fourth decade, suggesting that this variant may be a hypomorphic allele. RNA analysis using patient cells demonstrated that the c.-22-2A>C variant leads to expression of a novel GJB2 transcript with a slightly longer 5' UTR but otherwise normal coding region. The alternate transcript was shown to have reduced expression, but it is not clear if the lower expression is sufficient to lead to a phenotype (PS3_Supporting; PMID:24039984). In summary, the VCEP has used expert judgement to classify this variant as likely pathogenic for autosomal recessive hearing loss based on the ACMG/AMP criteria applied, as specified by the Hearing Loss Expert Panel: PM3_Very Strong, PP1, PS3_Supporting, BS1. LINK:https://erepo.genome.network/evrepo/ui/classification/CA6904346/MONDO:0019497/005

• Frequency:
  • Genomes: 𝑓 0.00058 (0 hom., cov: 33)
  • Exomes 𝑓: 0.00071 (2 hom.)
• Consequence: GJB2 NM_004004.6 splice_acceptor, intron
• Scores: Splicing: ADA: 1.000
• Clinical Significance: Likely pathogenic reviewed by expert panel P:19 U:2 B:2
• Conservation: PhyloP100: 6.71
• Publications: 17 publications found

Genes affected

GJB2 (HGNC:4284): (gap junction protein beta 2) This gene encodes a member of the gap junction protein family. The gap junctions were first characterized by electron microscopy as regionally specialized structures on plasma membranes of contacting adherent cells. These structures were shown to consist of cell-to-cell channels that facilitate the transfer of ions and small molecules between cells. The gap junction proteins, also known as connexins, purified from fractions of enriched gap junctions from different tissues differ. According to sequence similarities at the nucleotide and amino acid levels, the gap junction proteins are divided into two categories, alpha and beta. Mutations in this gene are responsible for as much as 50% of pre-lingual, recessive deafness. [provided by RefSeq, Oct 2008]

GJB2 Gene-Disease associations (from GenCC):

• Bart-Pumphrey syndrome

  Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: Genomics England PanelApp, Labcorp Genetics (formerly Invitae), G2P
• ichthyosis, hystrix-like, with hearing loss

  Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: G2P, Genomics England PanelApp
• keratoderma hereditarium mutilans

  Inheritance: AD Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Orphanet, Genomics England PanelApp, G2P
• palmoplantar keratoderma-deafness syndrome

  Inheritance: AD Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Genomics England PanelApp, Orphanet, G2P
• autosomal recessive nonsyndromic hearing loss 1A

  Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), Laboratory for Molecular Medicine, G2P, PanelApp Australia
• hearing loss, autosomal recessive

  Inheritance: AR Classification: DEFINITIVE, SUPPORTIVE Submitted by: Orphanet, ClinGen
• autosomal dominant keratitis-ichthyosis-hearing loss syndrome

  Inheritance: AD Classification: STRONG, MODERATE Submitted by: Genomics England PanelApp, Ambry Genetics
• autosomal dominant nonsyndromic hearing loss 3A

  Inheritance: AD Classification: STRONG Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae)
• autosomal dominant nonsyndromic hearing loss

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• KID syndrome

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

ENSG00000296095 (HGNC:):

ACMG classification

Our verdict: Likely_pathogenic. The variant received 0 ACMG points.

• PS3: For more information check the summary or visit ClinGen Evidence Repository.
• PM3: For more information check the summary or visit ClinGen Evidence Repository.
• PP1: For more information check the summary or visit ClinGen Evidence Repository.
• BS1: For more information check the summary or visit ClinGen Evidence Repository.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GJB2	NM_004004.6	c.-22-2A>C		splice_acceptor_variant, intron_variant	Intron 1 of 1	ENST00000382848.5	NP_003995.2
GJB2	XM_011535049.3	c.-22-2A>C		splice_acceptor_variant, intron_variant	Intron 1 of 1		XP_011533351.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GJB2	ENST00000382848.5	c.-22-2A>C		splice_acceptor_variant, intron_variant	Intron 1 of 1	1	NM_004004.6	ENSP00000372299.4
GJB2	ENST00000382844.2	c.-24A>C		5_prime_UTR_variant	Exon 1 of 1	6		ENSP00000372295.1
ENSG00000296095	ENST00000736390.1	n.232-4025A>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.000578 AC: 88 AN: 152182 Hom.: 0 Cov.: 33

Gnomad AFR AF: 0.0000965

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000916

Gnomad ASJ AF: 0.00490

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000764

Gnomad OTH AF: 0.000478

GnomAD2 exomes AF: 0.000607 AC: 151 AN: 248874 AF XY: 0.000704

Gnomad AFR exome AF: 0.0000617

Gnomad AMR exome AF: 0.000231

Gnomad ASJ exome AF: 0.00458

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.0000462

Gnomad NFE exome AF: 0.000827

Gnomad OTH exome AF: 0.000490

GnomAD4 exome AF: 0.000710 AC: 1034 AN: 1455754 Hom.: 2 Cov.: 30 AF XY: 0.000723 AC XY: 524 AN XY: 724646

African (AFR) AF: 0.000150 AC: 5 AN: 33350

American (AMR) AF: 0.000447 AC: 20 AN: 44714

Ashkenazi Jewish (ASJ) AF: 0.00425 AC: 111 AN: 26098

East Asian (EAS) AF: 0.00 AC: 0 AN: 39672

South Asian (SAS) AF: 0.00 AC: 0 AN: 86116

European-Finnish (FIN) AF: 0.0000187 AC: 1 AN: 53398

Middle Eastern (MID) AF: 0.000369 AC: 2 AN: 5422

European-Non Finnish (NFE) AF: 0.000753 AC: 834 AN: 1106836

Other (OTH) AF: 0.00101 AC: 61 AN: 60148

GnomAD4 genome AF: 0.000578 AC: 88 AN: 152300 Hom.: 0 Cov.: 33 AF XY: 0.000550 AC XY: 41 AN XY: 74480

African (AFR) AF: 0.0000962 AC: 4 AN: 41562

American (AMR) AF: 0.000915 AC: 14 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.00490 AC: 17 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5182

South Asian (SAS) AF: 0.00 AC: 0 AN: 4826

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10616

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.000764 AC: 52 AN: 68020

Other (OTH) AF: 0.000473 AC: 1 AN: 2112

Alfa AF: 0.000690 Hom.: 1

Bravo AF: 0.000608

ClinVar

Significance: Likely pathogenic

Submissions summary: Pathogenic:19 Uncertain:2 Benign:2

Revision: reviewed by expert panel

Submissions by phenotype

Autosomal recessive nonsyndromic hearing loss 1A Pathogenic:7 Uncertain:2

Mar 30, 2021

Neurogenetic Laboratory, Second Faculty of Medicine, Charles University

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Apr 08, 2016

Knight Diagnostic Laboratories, Oregon Health and Sciences University

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.-22-2A>C splice-acceptor variant in the GJB2 gene has been previously reported in 3 individuals within one generation of a single family affected with Deafness and Hearing Loss (Gandía et al., 2013). In all cases, this variant was observed in trans with the well-established pathogenic variant 35delG; however, these individuals experienced mild to moderate hearing loss that developed in the 3rd-4th decade of life (postlingual) (Gandía et al., 2013). Functional splicing studies have demonstrated this variant abolishes the canonical splice-acceptor site for intron 1 of GJB2. The loss of the canonical splice-site results in a longer transcript caused by an alternative splice-acceptor site that is within intron 1(Gandía et al., 2013). This variant is reported at low frequency in the population databases (Exome Sequencing Project = 0.058%; 1000 Genomes = 0%; and ExAC = 0.114%). Therefore, this collective evidence supports the classification of the c.-22-2A>C as a Pathogenic variant for Deafness and Hearing Loss. We have confirmed this finding in our laboratory using Sanger sequencing. -

Aug 16, 2018

Illumina Laboratory Services, Illumina

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The GJB2 c.-22-2A>C variant occurs in a canonical splice site (acceptor) and is therefore predicted to disrupt or distort the normal gene product. The c.-22-2A>C variant has been identified in a compound heterozygous state in four individuals with hearing loss. Three of these individuals were from a single Spanish family and exhibited mild, postlingual hearing impairment, with onset in the third to fourth decade of life (Gandía et al. 2013). The fourth individual was of Italian origin and displayed moderate hearing impairment of unspecified onset (Stanghellini et al. 2014). In all four cases, the c.-22-2A>C variant was found in trans with a well-known pathogenic null variant, c.35delG. The Spanish pedigree also included two normal hearing heterozygous individuals, consistent with a recessive pattern of inheritance. The variant was absent from 92 normal hearing control individuals and is reported at a frequency of 0.004539 in the Ashkenazi Jewish population of the Genome Aggregation Consortium. Quantitative RT-PCR experiments indicated that the variant abolishes the canonical acceptor splice site for intron 1 of GJB2 but that a reduced amount of transcript is produced via an alternative acceptor splice site (Gandía et al. 2013). Based on the evidence, the c.-22-2A>C allele is classified as likely pathogenic for autosomal recessive nonsyndromic hearing loss. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population. -

Apr 01, 2019

Counsyl

Significance: Uncertain significance

Review Status: no assertion criteria provided

Collection Method: clinical testing

This submission and the accompanying classification are no longer maintained by the submitter. For more information on current observations and classification, please contact variantquestions@myriad.com. -

Sep 18, 2024

Equipe Genetique des Anomalies du Developpement, Université de Bourgogne

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is located in a canonical splice acceptor site and is predicted to affect the mRNA product. It has been reported in patients with deafness and hearing loss (PMID 35864128, 34652575). It was reported as pathogenic multiple times in ClinVar. Based on the evidence outlined above, the variant was classified as likely pathogenic. -

Feb 01, 2024

Laboratory of Medical Genetics, National & Kapodistrian University of Athens

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: curation

- -

May 08, 2024

Laboratory of Prof. Karen Avraham, Tel Aviv University

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: research

In ClinVar: 5 'Likely pathogenic' and 2 'Pathogenic' submissions -

Jul 16, 2023

Victorian Clinical Genetics Services, Murdoch Childrens Research Institute

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as Likely pathogenic. Following criteria are met: 0102 - Loss of function is a known mechanism of disease in this gene and is associated with both deafness and skin conditions (OMIM). Dominant negative is also a suggested mechanism (PMID: 28428247). (I) 0108 - This gene is associated with both recessive and dominant disease. The autosomal dominant diseases are commonly associated with pathogenic missense variants. The autosomal recessive disease is associated with bi-allelic loss-of-function variants and includes missense and protein truncating variants (NIH Genetics Home Reference, PMID: 12792423). (I) 0112 - The condition associated with this gene has incomplete penetrance (PMID:31160754). (I) 0115 - Variants in this gene are known to have variable expressivity. Severity can range from mild to profound with intrafamilial variability also commonly seen. Commonly, truncating variants are associated to a more severe hearing loss (PMID: 20301449). (I) 0209 - Splice site variant proven to affect splicing of the transcript with uncertain effect on protein sequence. RT-PCR performed on patient saliva RNA demonstrated that this variant abolishes the use of the WT acceptor splice site and introduces the use of two alternate acceptor splice sites, both of which are predicted to keep the coding region intact and are expressed at lower levels compared to the WT transcript. The residual expression of these two alternate transcripts has been hypothesized to explain for the milder phenotype observed in affected individuals although the exact effect is currently unknown. Additionally, as specific protein studies were not performed, the effect of the variant on protein sequence is still unclear (PMID: 24039984). (SP) 0251 - This variant is heterozygous. (I) 0304 - Variant is present in gnomAD (v2) <0.01 for a recessive condition (162 heterozygotes, 0 homozygotes). (SP) 0801 - This variant has very strong previous evidence of pathogenicity in unrelated individuals. This variant has been classified as likely pathogenic by the ClinGen Hearing Loss Variant Curation Expert Panel and associated with mild and moderate autosomal recessive non-syndromic hearing loss (ClinVar, PMID: 31053783). (SP) 0903 - This variant has limited evidence for segregation with disease. This variant has been shown to co-segregate with the NM_004004.6(GJB2):c.35del; p.(Gly12Valfs*2) variant in three siblings with mild postlingual hearing loss (PMID: 24039984). (SP) 1208 - Inheritance information for this variant is not currently available in this individual. (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign -

Nov 04, 2024

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant summary: GJB2 c.-22-2A>C is located in a canonical splice-site and is predicted to affect mRNA splicing resulting in a significantly altered protein due to either exon skipping, shortening, or inclusion of intronic material. Several computational tools predict a significant impact on normal splicing: Five predict the variant abolishes the canonical 3' acceptor site. At least one publication reports experimental evidence that this variant leads to alternative splicing and two novel transcripts which may express some level of wild type GJB2 (Gandia_2013). However, the tissue type used in this study, saliva, may not represent the most optimal tissue type to base evidence supporting residual transcript expression in an affected tissue. A cochlear tissue, or another ear expressed tissue type may be more informative. The variant allele was found at a frequency of 0.00061 in 251058 control chromosomes. This frequency is not significantly higher than estimated for a pathogenic variant in GJB2 causing Autosomal Recessive Non-Syndromic Hearing Loss (0.00061 vs 0.025), allowing no conclusion about variant significance. c.-22-2A>C has been reported in the literature as a compound heterozygous genotype with c.35delG in individuals predominantly reported to have postlingual mild-moderate hearing loss (example, Gandia_2013, Burke_2016, Stanghellini_2014, Cabanillas_2018, Buonfigilio_2020). Although one conference abstract showed that there was no significant difference in allelic or genotypic frequencies between patient and control groups in an Italian subpopulation, the authors did state that the disease-causing effect of this variant when in trans with a truncating mutation cannot be excluded (Gandia_2013). Furthermore, at-least one recent study re-evaluated this variant as "Likely Pathogenic" reporting the ACMG/AMP criteria coupled with hearing-loss-gene-specific criteria of the ClinGen hearing loss expert panel (Buonfigilio_2020). These data indicate that the variant is likely to be associated with disease. To our knowledge no direct experimental evidence evaluating a variant specific impact on protein function and assembly have been reported. The following publications have been ascertained in the context of this evaluation (PMID: 33096615, 26778469, 29986705, 24039984, 27057829, 35864128, 34652575, 31195736, 34062854, 25401782). ClinVar contains an entry for this variant (Variation ID: 375406). Based on the evidence outlined above, the variant was classified as likely pathogenic for postlingual mild-moderate hearing loss. -

not provided Pathogenic:6

Apr 11, 2024

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The GJB2 c.-22-2A>C variant (rs201895089; ClinVar ID: 375406) is reported in the literature in multiple individuals affected with mild-to-moderate hearing loss who carried a second pathogenic GJB2 variant in trans (Buonfiglio 2020, Gandia 2013, Safka Brokova 2021, Stanghellini 2014). The c.-22-2A>C variant segregated with disease in multiple affected members of a family with hearing loss (Gandia 2013). This variant is found in the Ashkenazi Jewish population with an allele frequency of 0.45% (47/10,344 alleles) in the Genome Aggregation Database (v2.1.1). This variant disrupts the canonical splice acceptor site of intron 1, which is likely to negatively impact gene function. Indeed, functional analysis confirm an effect on splicing; however, the overall impact on protein expression is not well defined (Gandia 2013). Based on available information, this variant is considered to be likely pathogenic. References: Buonfiglio P et al. GJB2 and GJB6 Genetic Variant Curation in an Argentinean Non-Syndromic Hearing-Impaired Cohort. Genes (Basel). 2020 Oct 21;11(10):1233. PMID: 33096615. Gandia M et al. A novel splice-site mutation in the GJB2 gene causing mild postlingual hearing impairment. PLoS One. 2013 Sep 6;8(9):e73566. PMID: 24039984. Safka Brozkova D et al. The Cause of Hereditary Hearing Loss in GJB2 Heterozygotes-A Comprehensive Study of the GJB2/DFNB1 Region. Genes (Basel). 2021 May 1;12(5):684. PMID: 34062854. Stanghellini I et al. New and rare GJB2 alleles in patients with nonsyndromic sensorineural hearing impairment: a genotype/auditory phenotype correlation. Genet Test Mol Biomarkers. 2014 Dec;18(12):839-44. PMID: 25401782. -

Jan 24, 2024

Athena Diagnostics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is expected to severely impact normal RNA splicing, and consequently, protein structure and/or function. The frequency of this variant in the general population is consistent with pathogenicity. (http://gnomad.broadinstitute.org) This variant has been identified in at least one individual with autosomal recessive hearing loss and appears to be associated with disease in at least one family. -

May 11, 2023

Revvity Omics, Revvity

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Jan 30, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This sequence change falls in intron 1 of the GJB2 gene. It does not directly change the encoded amino acid sequence of the GJB2 protein. It affects a nucleotide within the consensus splice site. This variant is present in population databases (rs201895089, gnomAD 0.5%), and has an allele count higher than expected for a pathogenic variant. This variant has been observed in individual(s) with autosomal recessive deafness (PMID: 24039984, 29311818). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. It has also been observed to segregate with disease in related individuals. This variant has been reported in individuals with postlingual mild-moderate hearing loss (PMID: 24039984, 25401782, 29311818, 19814620, 34062854). Individuals homozygous for this variant may or may not be affected. ClinVar contains an entry for this variant (Variation ID: 375406). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. -

Oct 01, 2023

CeGaT Center for Human Genetics Tuebingen

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

GJB2: PM3:Very Strong, PP1:Strong, PM2:Supporting, PS3:Supporting -

May 16, 2025

GeneDx

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Published functional studies using patient cells demonstrate the use of two alternative cryptic splice acceptor sites in lieu of the destroyed canonical splice acceptor site, resulting in a longer 5'UTR and reduced expression of the alternate transcript; however, the coding regions remain intact and it is not clear if the lower expression is sufficient to have a clinical effect (PMID: 24039984); In silico analysis supports a deleterious effect on splicing; This variant is associated with the following publications: (PMID: 34428318, 30455902, 30311386, 29754767, 34426522, 34062854, 29016196, 19814620, 33096615, 34652575, 31053783, 31980526, DiStefano2020[paper], 24039984, 26778469, 34325055, 34308104, 36651276, 36979683, 36837553, 38397306) -

Nonsyndromic genetic hearing loss Pathogenic:2

Aug 31, 2020

INGEBI, INGEBI / CONICET

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Based on ACMG/AMP guidelines and Hearing Loss Expert Panel specific criteria: the filtering allele frequency of the c.-22-2A>C variant in the GJB2 gene is 0.35% (of 47/10344 alleles Ashkenazi Jewish with chromosomes with 95% CI) from Genome Aggregation Database calculated by using inverse allele frequency at https://www.cardiodb.org/allelefrequencyapp/),applying to BS1 rule. The c.-22-2A>C variant has been detected in at least 4 patients with hearing loss in trans with the pathogenic c.35delG variant (PMID: 25401782, 24039984; Invitae internal data, SCV000935680.2; Laboratory of Physiology and Genetics of Hearing internal data described by ClinGen HL-EP). In addition to this, new evidence is considered since the c.-22-2A>C variant was reported in trans with p.Leu90Pro in a hearing impaired patient (PMID: 19814620, nomenclature issue checked with author: the variant called c.-24A>C in that paper is indeed c.-22-2A>C). In all those genotypes detected, patients exhibited postlingual mild-moderate hearing loss. Since this variant has a high frequency in population databases, the strength of PM3 rule was downgraded from very strong to moderate (PM3_Moderate). The c.[-22-2A>C];[35delG] genotype segregated in two affected and two unaffected members of the family (PP1_Strong; PMID: 24039984). RNA analysis showed that patients with the c.-22-2A>C variant used two alternative splice sites leading to slightly longer 5' UTR transcripts containing normal coding region but with alternated expression. This variant is suspected to be a hypomorphic allele resulting in a postlingual mild-moderate hearing loss phenotype (PS3_Supporting; PMID: 24039984). Therefore, this variant meets criteria to be classified as likely pathogenic for autosomal recessive non-syndromic hearing loss (BS1, PM3_Moderate, PP1_Strong, PS3_Supporting). -

Apr 12, 2021

ClinGen Hearing Loss Variant Curation Expert Panel

Significance: Likely pathogenic

Review Status: reviewed by expert panel

Collection Method: curation

The filtering allele frequency of the c.-22-2A>C variant in the GJB2 gene is 0.35% for Ashkenazi Jewish chromosomes in gnomAD v2.1.1 (95% CI of 47/10344), which meets the allele frequency threshold defined by the ClinGen Hearing Loss Expert Panel for considering strong evidence against pathogenicity for autosomal recessive hearing loss variants (BS1). However, based on the evidence outlined below, the ClinGen Hearing Loss Expert Panel believes that the evidence for the pathogenicity of this variant for nonsyndromic hearing loss outweighs its high allele frequency in population databases. Therefore, the BS1 code will not contribute to the overall classification. The c.-22-2A>C variant in the GJB2 gene has been detected in at least 9 patients with hearing loss in trans with the pathogenic c.35delG variant (PM3_Very Strong; PMID: 25401782, 24039984, 33096615; Invitae internal data, SCV000935680.2; Children’s Hospital of Philadelphia internal data, Molecular Otolaryngology and Renal Research Laboratories internal data) and one individual with the the p.Leu90Pro variant suspected in trans (PMID: 19814620). Phase was confirmed in at least 6 of these 10 observations.This variant has been reported to segregate with hearing loss in at least 2 family members (PP1; PMID: 24039984). It was also identified in the heterozygous state without a second variant in 8 individuals with hearing loss, and in the biallelic state (with c.35delG) in one individual with reportedly normal hearing (GeneDx, ARUP internal data, SCV000680741.2, SCV000603828.1). Of note, the severity of hearing loss is reported to be mild-moderate in affected probands, some with onset in the third to fourth decade, suggesting that this variant may be a hypomorphic allele. RNA analysis using patient cells demonstrated that the c.-22-2A>C variant leads to expression of a novel GJB2 transcript with a slightly longer 5' UTR but otherwise normal coding region. The alternate transcript was shown to have reduced expression, but it is not clear if the lower expression is sufficient to lead to a phenotype (PS3_Supporting; PMID: 24039984). In summary, the VCEP has used expert judgement to classify this variant as likely pathogenic for autosomal recessive hearing loss based on the ACMG/AMP criteria applied, as specified by the Hearing Loss Expert Panel: PM3_Very Strong, PP1, PS3_Supporting, BS1. -

not specified Pathogenic:1

Jan 18, 2024

Genomic Medicine Center of Excellence, King Faisal Specialist Hospital and Research Centre

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: research

- -

Autosomal dominant keratitis-ichthyosis-hearing loss syndrome;C0265964:Mutilating keratoderma;C0266004:Knuckle pads, deafness AND leukonychia syndrome;C1835672:Palmoplantar keratoderma-deafness syndrome;C1865234:Ichthyosis, hystrix-like, with hearing loss;C2673759:Autosomal recessive nonsyndromic hearing loss 1A;C2675750:Autosomal dominant nonsyndromic hearing loss 3A Pathogenic:1

Apr 23, 2024

Fulgent Genetics, Fulgent Genetics

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

GJB2-related disorder Pathogenic:1

Feb 06, 2024

PreventionGenetics, part of Exact Sciences

Significance: Likely pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

The GJB2 c.-22-2A>C variant is located in the 5' untranslated region. This variant has been reported in at least four patients with mild to moderate hearing loss from two families in the compound heterozygous state with a second pathogenic variant (Gandía et al. 2013. PubMed ID: 24039984; Stanghellini et al. 2014. PubMed ID: 25401782). This variant has also been shown to disrupt the canonical splice acceptor site, although some transcripts with an intact coding region were detected (Gandía et al. 2013. PubMed ID: 24039984). This variant is reported in 0.45% of alleles in individuals of Ashkenazi Jewish descent in gnomAD, which is higher than expected for a fully penetrant autosomal recessive pathogenic variant in this gene. This variant is classified by the ClinGen Hearing Loss Variant Curation Expert Panel as likely pathogenic for autosomal recessive hearing loss, noting the mild to moderate phenotype in some patients (https://www.ncbi.nlm.nih.gov/clinvar/variation/375406/). This variant is interpreted as likely pathogenic. -

Mutilating keratoderma;C0266004:Knuckle pads, deafness AND leukonychia syndrome;C1835672:Palmoplantar keratoderma-deafness syndrome Pathogenic:1

Jul 26, 2023

Department of Pathology and Laboratory Medicine, Sinai Health System

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: research

- -

Ichthyosis, hystrix-like, with hearing loss Benign:1

Aug 23, 2017

Illumina Laboratory Services, Illumina

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases was too high to be consistent with this variant causing disease. Therefore, this variant is classified as benign. -

Autosomal dominant nonsyndromic hearing loss 3A Benign:1

Aug 23, 2017

Illumina Laboratory Services, Illumina

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to rule this variant out of causing disease. Therefore, this variant is classified as benign. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.45
CADD	Pathogenic	27
DANN	Uncertain	0.99
PhyloP100		6.7
PromoterAI		-0.021	Neutral
Mutation Taster		=56/244	disease causing

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	1.0
dbscSNV1_RF	Pathogenic	0.92
SpliceAI score (max)		0.91		Details are displayed if max score is > 0.2
DS_AG_spliceai		0.23		Position offset: 36
DS_AL_spliceai		0.91		Position offset: -2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs201895089; hg19: chr13-20763744;