rs80338940

chr13-20192782-C-T

Variant summary

Our verdict is Pathogenic. Variant got 16 ACMG points: 16P and 0B. PVS1_Strong PP3_Strong PP5_Very_Strong

The NM_004004.6(GJB2):c.-23+1G>A variant causes a splice donor change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00028 in 153,332 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Likely pathogenic (★★).

• Frequency:
  • Genomes: 𝑓 0.00028 (0 hom., cov: 33)
  • Exomes 𝑓: 0.00088 (0 hom.)
• Consequence: GJB2 NM_004004.6 splice_donor
• Scores: Splicing: ADA: 1.000
• Clinical Significance: Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:37
• Conservation: PhyloP100: 1.12

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]

ACMG classification

Verdict is Pathogenic. Variant got 16 ACMG points.

• PVS1: Splicing variant, NOT destroyed by nmd, known LOF gene, truncates exone, which is 0.22760646 fraction of the gene.
• PP3: Splicing scoreres supports a deletorius effect: Scorers claiming Pathogenic: dbscSNV1_ADA, dbscSNV1_RF, max_spliceai. No scorers claiming Uncertain. No scorers claiming Benign.
• PP5: Variant 13-20192782-C-T is Pathogenic according to our data. Variant chr13-20192782-C-T is described in ClinVar as [Likely_pathogenic]. Clinvar id is 17029.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr13-20192782-C-T is described in Lovd as [Likely_pathogenic]. Variant chr13-20192782-C-T is described in Lovd as [Pathogenic]. Variant chr13-20192782-C-T is described in Lovd as [Pathogenic]. Variant chr13-20192782-C-T is described in Lovd as [Likely_pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GJB2	NM_004004.6	c.-23+1G>A		splice_donor_variant		ENST00000382848.5
GJB2	XM_011535049.3	c.-844G>A		5_prime_UTR_variant	1/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GJB2	ENST00000382848.5	c.-23+1G>A		splice_donor_variant		1	NM_004004.6	P1

Frequencies

GnomAD3 genomes AF: 0.000276 AC: 42 AN: 152092 Hom.: 0 Cov.: 33

Gnomad AFR AF: 0.0000483

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000387

Gnomad SAS AF: 0.00228

Gnomad FIN AF: 0.0000944

Gnomad MID AF: 0.00321

Gnomad NFE AF: 0.000324

Gnomad OTH AF: 0.00143

GnomAD4 exome AF: 0.000883 AC: 1 AN: 1132 Hom.: 0 Cov.: 0 AF XY: 0.00142 AC XY: 1 AN XY: 702

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00183

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.000276 AC: 42 AN: 152200 Hom.: 0 Cov.: 33 AF XY: 0.000349 AC XY: 26 AN XY: 74418

Gnomad4 AFR AF: 0.0000481

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000388

Gnomad4 SAS AF: 0.00228

Gnomad4 FIN AF: 0.0000944

Gnomad4 NFE AF: 0.000324

Gnomad4 OTH AF: 0.00142

Alfa AF: 0.000162 Hom.: 0

Bravo AF: 0.000178

Asia WGS AF: 0.00262 AC: 9 AN: 3452

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:37

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Autosomal recessive nonsyndromic hearing loss 1A Pathogenic:15

Pathogenic, criteria provided, single submitter	clinical testing	Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center	Mar 26, 2024	- -
Pathogenic, no assertion criteria provided	literature only	OMIM	Sep 01, 2011	- -
Pathogenic, no assertion criteria provided	literature only	GeneReviews	Jul 14, 2011	- -
Pathogenic, criteria provided, single submitter	clinical testing	MGZ Medical Genetics Center	Jul 11, 2022	- -
Pathogenic, criteria provided, single submitter	clinical testing	Genomic Diagnostic Laboratory, Division of Genomic Diagnostics, Children's Hospital of Philadelphia	May 09, 2017	- -
Pathogenic, criteria provided, single submitter	clinical testing	Myriad Genetics, Inc.	Dec 24, 2019	NM_004004.5(GJB2):c.-23+1G>A is classified as pathogenic in the context of GJB2-related DFNB1 nonsyndromic hearing loss and deafness. Sources cited for classification include the following: PMID 21776002. Classification of NM_004004.5(GJB2):c.-23+1G>A is based on the following criteria: The variant is located at a canonical splice site, is expected to disrupt gene function and is reported in individuals with the relevant phenotype. Please note: this variant was assessed in the context of healthy population screening. -
Pathogenic, no assertion criteria provided	clinical testing	Knight Diagnostic Laboratories, Oregon Health and Sciences University	Feb 11, 2015	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	Foundation for Research in Genetics and Endocrinology, FRIGE's Institute of Human Genetics	Apr 28, 2023	A heterozygous 5’ splice site variant in intron 1 of the GJB2 gene that affects the invariant GT donor splice site downstream of exon 1 was detected. This variant has not been reported in the 1000 genomes and gnomdAD (v2) databases and has a minor allele frequency of 0.03% and 0.02% in the gnomAD (v3.1) and topmed databases, respectively. The in silico prediction of the variant is damaging by MutationTaster2. The reference base is conserved across mammals. In summary, the variant meets our criteria to be classified as likely pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	Johns Hopkins Genomics, Johns Hopkins University	Apr 28, 2023	This GJB2 canonical splice variant has been reported in the homozygous or compound heterozygous state in multiple unrelated individuals with autosomal recessive deafness 1A. This variant (rs80338940) is present in a large population dataset (gnomAD v3.1.2: 42/152092 total alleles; 0.03%; no homozygotes), and has been reported in ClinVar (Variation ID 17029). The variant destroys a canonical splice donor site, is predicted to cause abnormal gene splicing and has supporting functional evidence1. We consider c.-23+1G>A in GJB2 to be pathogenic. -
Pathogenic, no assertion criteria provided	case-control	Genetic Testing Center for Deafness, Department of Otolaryngology Head & Neck Surgery, Institute of Otolaryngology, Chinese PLA General Hospital	Feb 26, 2019	- -
Pathogenic, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Oct 24, 2016	Variant summary: The GJB2 c.-23+1G>A variant (alternatively also known as IVS1+1G>A, -3170G>A, -3201G>A, -3179G>A, and -3172G>A) involves the alteration of the invariant splice donor site in intron 1. 5/5 splice prediction tools predict that this variant eliminates the 5' splicing donor site. The prediction result was confirmed by a functional study; RNA isolated from lymphocytes from the proband carrying c.-23-1G>A variant and subsequent sequencing of cDNA showed no transcript from this allele (Shahin_2002). This variant was found in 21/4256 control chromosomes at a frequency of 0.0049342, which does not exceed the estimated maximal expected allele frequency of a pathogenic GJB2 variant (0.025). This variant has been reported as one of the common pathogenic variants causing ARNSHL in literature with consistent genotype-phenotype data. The variant has also been postulated to originate from and to have a founder effect in central Asia (Barashkov_2011). Multiple clinical diagnostic laboratories/reputable databases have classified this variant as pathogenic. Taken together, this variant is classified as Pathogenic. -
Pathogenic, no assertion criteria provided	clinical testing	Natera, Inc.	Sep 16, 2020	- -
Pathogenic, criteria provided, single submitter	clinical testing	Integrating Genomics into Medicine, Frazer Institute, University Of Queensland	Jun 02, 2023	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	Foundation for Research in Genetics and Endocrinology, FRIGE's Institute of Human Genetics	Apr 04, 2023	A heterozygous 5’ splice site variant in intron 1 of the GJB2 gene that affects the invariant GT donor splice site downstream of exon 1 (c.-23+1G>A; ENST00000382848.5) was detected. The observed variant has previously been reported (as IVS1+1G>A) in patients affected with hearing loss [PMID: 27843504, ClinVar: VCV000017029.72]. This variant has not been reported in the 1000 genomes and gnomdAD (v2) databases and has a minor allele frequency of 0.03% and 0.02% in the gnomAD (v3.1) and topmed databases, respectively. The in-silico prediction of the variant is damaging by MutationTaster2. The reference base is conserved across mammals. In summary, the variant meets our criteria to be classified as likely pathogenic. -
Pathogenic, criteria provided, single submitter	research	King Laboratory, University of Washington	Aug 01, 2020	GJB2 c.-23+1G>A is homozygous in a Palestinian child with severe to profound hearing loss (Abu Rayyan 2020). Based on analysis of RNA from the patient, no transcript from the mutant allele was detectable (PMID: 11935342). The variant is not present in 1300 Palestinian controls and absent from gnomAD v2.1.1. -

not provided Pathogenic:9

Pathogenic, criteria provided, single submitter	clinical testing	Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen	Sep 15, 2021	- -
Pathogenic, no assertion criteria provided	clinical testing	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	-	- -
Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Nov 03, 2021	Canonical splice site variant in a gene for which loss-of-function is a known mechanism of disease; Published functional studies indicate that this variant disrupts splicing and results in no gene transcription (Shahin et al., 2002); Also known IVS1+1G>A; This variant is associated with the following publications: (PMID: 24840842, 24959830, 25012701, 11935342, 31162818, 16650079, 32708339, 10218527, 24793888, 27843504, 27481527, 31160754, 21776002, 31980526, 32747562, 33096615, 29062245, 30030956, 30487145, 31346875, 31195736, 29907799, 30344259, 31541171, 30275481, 33105617) -
Pathogenic, criteria provided, single submitter	clinical testing	Invitae	Jan 31, 2024	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 (rs80338940, gnomAD 0.03%). This variant has been observed in individual(s) with deafness (PMID: 10218527, 11935342, 21776002, 24840842, 24959830, 27481527, 27843504). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. It is commonly reported in individuals of Yakut ancestry (PMID: 21776002). ClinVar contains an entry for this variant (Variation ID: 17029). Studies have shown that this variant alters GJB2 gene expression (PMID: 11935342). 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. For these reasons, this variant has been classified as Pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	Revvity Omics, Revvity	Dec 21, 2023	- -
Pathogenic, criteria provided, single submitter	clinical testing	Athena Diagnostics	Mar 23, 2022	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). The variant is a common founder originating from Eastern Siberia (PMID: 21776002). This variant is also referred to as IVS1+1G>A, -3170G>A, -3201G>A, -3179G>A, or -3172G>A in published literature. Assessment of experimental evidence suggests this variant results in abnormal protein function. RNA studies performed on patient lymphocytes yielded no detectable transcript (PMID: 11935342). In multiple individuals, this variant has been seen with a single recessive pathogenic variant in the same gene, suggesting this variant may also be pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Aug 01, 2017	- -
Pathogenic, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	Feb 12, 2021	The GJB2 c.-23+1G>A variant (rs80338940), also known as IVS-1+1G>A, has been reported in individuals with autosomal recessive deafness (Barashkov 2011, Denoyelle 1999, Shahin 2002). Functional characterization of the variant indicates an absence of detectable transcript in the patient (Shahin 2002). The variant is listed as pathogenic in ClinVar (Variation ID: 17029), and observed 5 times in the Genome Aggregation Database general population database (5/30850 alleles). The variant is located in the splice consensus site, and computational algorithms (GeneSplicer, Human Splicing Finder, MaxEntScan, MutationTaster, NetGene2, NNSplice, SpliceSiteFinder-like) predict the loss of the canonical splice donor. Based on the above information, the variant is classified as pathogenic. References: Barashkov N et al. Autosomal recessive deafness 1A (DFNB1A) in Yakut population isolate in Eastern Siberia: extensive accumulation of the splice site mutation IVS1+1G>A in GJB2 gene as a result of founder effect. J Hum Genet. 2011; 56(9):631-9. Denoyelle F et al. Clinical features of the prevalent form of childhood deafness, DFNB1, due to a connexin-26 gene defect: implications for genetic counselling. Lancet. 1999; 353(9161):1298-303. Shahin H et al. Genetics of congenital deafness in the Palestinian population: multiple connexin 26 alleles with shared origins in the Middle East. Hum Genet. 2002; 110(3):284-9. -
Pathogenic, no assertion criteria provided	clinical testing	Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	-	- -

Autosomal dominant nonsyndromic hearing loss 3A Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	Baylor Genetics	Mar 23, 2022	- -
Pathogenic, criteria provided, single submitter	clinical testing	Lifecell International Pvt. Ltd	-	A Heterozygous Splice site donor variant c.-23+1G>A in Exon 1 of the GJB2 gene that results in the amino acid substitution was identified. The observed variant has a maximum allele frequency is novel in gnomAD exomes and 0.00019% in genomes, respectively. The severity of the impact of this variant on the protein is high, based on the effect of the protein and REVEL score . Rare Exome Variant Ensemble Learner (REVEL) is an ensembl method for predicting the pathogenicity of missense variants based on a combination of scores from 13 individual tools: MutPred, FATHMM v2.3, VEST 3.0, PolyPhen-2, SIFT, PROVEAN, MutationAssessor, MutationTaster, LRT, GERP++, SiPhy, phyloP, and phastCons. The REVEL score for an individual missense variant can range from 0 to 1, with higher scores reflecting greater likelihood that the variant is disease-causing. ClinVar has also classified this variant as Pathogenic [Variation ID: 17029]. The literature have been suggesting that, heterozygosity for a GJB2 or GJB6 mutation connotes carrier status for NSHL and rarely can cause autosomal dominant hearing loss by Vassos Neocleous et al., 2014. For these reasons, this variant has been classified as Pathogenic. -

Hearing impairment Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	Department of Otolaryngology – Head & Neck Surgery, Cochlear Implant Center	Apr 12, 2021	PVS1_Strong, PS1_Strong, PM3_Moderate, BP4_Supporting -
Pathogenic, criteria provided, single submitter	clinical testing	Genetic Services Laboratory, University of Chicago	Feb 08, 2013	- -

Hearing loss Pathogenic:1

Pathogenic, no assertion criteria provided

clinical testing

Clinical Molecular Genetics Laboratory, Johns Hopkins All Children's Hospital

Aug 14, 2017

- -

Nonsyndromic genetic hearing loss Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

INGEBI, INGEBI / CONICET

Aug 21, 2020

Based on ACMG/AMP guidelines and Hearing Loss Expert Panel specific criteria: the c.-23+1G>A variant in GJB2 gene is absent from population databases (gnomAD, GO-ESP, 1000 genomes) meeting PM2 criteria. This type of variant is predicted to generate a loss of the donor splicing site in GJB2 gene , which is a known mechanism of disease (PVS1). The c.-23+1G>A variant has been identified in trans with at least 4 pathogenic variants in hearing loss patients applying to PM3_VeryStrong rule (PMID: 10218527, 11313763, 16380907). It was demonstrated that this genetic variant disrupted splicing, yielding no detectable message by sequencing the cDNA from lymphoblastoid cell line of J3 from mutant allele, meeting PS3_Supporting criteria (PMID: 11935342). Therefore, the c.23-23+1G>A variant meets criteria to be classified as pathogenic for autosomal recessive non-syndromic hearing loss (PM2, PVS1, PM3_VerySrong, PS3_Supporting) -

GJB2-related disorder Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

Feb 14, 2024

The GJB2 c.-23+1G>A variant is located in the 5' untranslated region. This variant is also described as c.-3170G>A or IVS1+1G>A. This variant has been reported to be causative for autosomal recessive nonsyndromic hearing loss (Denoyelle et al. 1999. PubMed ID: 10218527; Barashkov et al. 2011. PubMed ID: 21776002; Barashkov et al. 2014. PubMed ID: 24959830). This variant is reported in 0.032% of alleles in individuals of European (Non-Finnish) descent in gnomAD. This variant is interpreted as pathogenic. -

Autosomal recessive nonsyndromic hearing loss 1A;C2675235:Autosomal recessive nonsyndromic hearing loss 1B Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Baylor Genetics

-

- -

Autosomal recessive nonsyndromic hearing loss 104 Pathogenic:1

Pathogenic, criteria provided, single submitter

not provided

Institute of Human Genetics, University Hospital of Duesseldorf

-

- -

Hearing loss, autosomal recessive Pathogenic:1

Likely pathogenic, no assertion criteria provided

research

University of Washington Center for Mendelian Genomics, University of Washington

-

- -

Autosomal dominant keratitis-ichthyosis-hearing loss syndrome;C0265964:Mutilating keratoderma;C0266004:Knuckle pads, deafness AND leukonychia syndrome;C1835672:Palmoplantar keratoderma-deafness syndrome;C1844678:X-linked mixed hearing loss with perilymphatic gusher;C1865234:Ichthyosis, hystrix-like, with hearing loss;C2673759:Autosomal recessive nonsyndromic hearing loss 1A;C2675750:Autosomal dominant nonsyndromic hearing loss 3A Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Fulgent Genetics, Fulgent Genetics

Jul 06, 2021

- -

Rare genetic deafness Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Jun 30, 2022

The c.-23+1G>A variant in GJB2 has been reported in many probands with hearing loss (Denoyelle 1999 PMID: 10218527, Shahin 2002 PMID: 11935342, Sirmaci 2006 PMID: 17406097, Yuan 2010 PMID: 21122151, Barashkov 2011 PMID: 21776002). Most of these probands were homozygous or compound heterozygous. In addition, functional studies have shown that this variant disrupts splicing, yielding no detectable mRNA (Shahin 2002 PMID: 11935342). In summary, this variant meets our criteria to be classified as pathogenic. ACMG/AMP Criteria applied: PM3_VeryStrong; PS3. -

Ear malformation Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Kariminejad - Najmabadi Pathology & Genetics Center

Jul 10, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Uncertain	23
DANN	Benign	0.93

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	1.0
dbscSNV1_RF	Pathogenic	0.84
SpliceAI score (max)		1.0		Details are displayed if max score is > 0.2
DS_DL_spliceai		1.0		Position offset: 1

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

Publications

LitVar

Other links and lift over

dbSNP: rs80338940; hg19: chr13-20766921;