13-20189333-G-C

Position:

• chr13-20189333-G-C

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 2P and 13B. PM1 BP4_Strong BP6_Very_Strong BS2_Supporting

The NM_004004.6(GJB2):​c.249C>G​(p.Phe83Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00272 in 1,614,086 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

• Frequency:
  • Genomes: 𝑓 0.0014 (0 hom., cov: 33)
  • Exomes 𝑓: 0.0029 (6 hom.)
• Consequence: GJB2 NM_004004.6 missense
• Clinical Significance: Benign/Likely benign criteria provided, multiple submitters, no conflicts B:17
• Conservation: PhyloP100: -3.35

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 Benign. Variant got -11 ACMG points.

• PM1: In a helix (size 29) in uniprot entity CXB2_HUMAN there are 23 pathogenic changes around while only 1 benign (96%) in NM_004004.6
• BP4: Computational evidence support a benign effect (MetaRNN=0.032549888).
• BP6: Variant 13-20189333-G-C is Benign according to our data. Variant chr13-20189333-G-C is described in ClinVar as [Likely_benign]. Clinvar id is 44732.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr13-20189333-G-C is described in Lovd as [Likely_benign].
• BS2: High Homozygotes in GnomAdExome4 at 6 AD,AR,Digenic geneVariant has number of homozygotes lower than other variant known as pathogenic in the gene, so the strength is limited to Supporting.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GJB2	NM_004004.6	c.249C>G	p.Phe83Leu	missense_variant	2/2	ENST00000382848.5	NP_003995.2
GJB2	XM_011535049.3	c.249C>G	p.Phe83Leu	missense_variant	2/2		XP_011533351.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GJB2	ENST00000382848.5	c.249C>G	p.Phe83Leu	missense_variant	2/2	1	NM_004004.6	ENSP00000372299.4
GJB2	ENST00000382844.2	c.249C>G	p.Phe83Leu	missense_variant	1/1	6		ENSP00000372295.1

Frequencies

GnomAD3 genomes AF: 0.00141 AC: 214 AN: 152172 Hom.: 0 Cov.: 33

Gnomad AFR AF: 0.000652

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000393

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.000566

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00250

Gnomad OTH AF: 0.00239

GnomAD3 exomes AF: 0.00167 AC: 420 AN: 251342 Hom.: 0 AF XY: 0.00159 AC XY: 216 AN XY: 135860

Gnomad AFR exome AF: 0.000615

Gnomad AMR exome AF: 0.000318

Gnomad ASJ exome AF: 0.0000992

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.000417

Gnomad NFE exome AF: 0.00332

Gnomad OTH exome AF: 0.00196

GnomAD4 exome AF: 0.00286 AC: 4178 AN: 1461796 Hom.: 6 Cov.: 33 AF XY: 0.00283 AC XY: 2056 AN XY: 727192

Gnomad4 AFR exome AF: 0.000508

Gnomad4 AMR exome AF: 0.000447

Gnomad4 ASJ exome AF: 0.000115

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.000619

Gnomad4 NFE exome AF: 0.00351

Gnomad4 OTH exome AF: 0.00329

GnomAD4 genome AF: 0.00141 AC: 214 AN: 152290 Hom.: 0 Cov.: 33 AF XY: 0.00126 AC XY: 94 AN XY: 74474

Gnomad4 AFR AF: 0.000650

Gnomad4 AMR AF: 0.000392

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.000566

Gnomad4 NFE AF: 0.00250

Gnomad4 OTH AF: 0.00236

Alfa AF: 0.00209 Hom.: 0

Bravo AF: 0.00139

TwinsUK AF: 0.00458 AC: 17

ALSPAC AF: 0.00493 AC: 19

ESP6500AA AF: 0.000681 AC: 3

ESP6500EA AF: 0.00326 AC: 28

ExAC AF: 0.00180 AC: 219

Asia WGS AF: 0.000289 AC: 1 AN: 3478

EpiCase AF: 0.00224

EpiControl AF: 0.00255

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:17

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:7

Benign, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	Sep 13, 2022	- -
Likely benign, criteria provided, single submitter	clinical testing	GeneDx	Jul 23, 2020	This variant is associated with the following publications: (PMID: 22995991, 9600457, 26778469, 30828346, 25262649, 20956747, 15070423, 12505163, 24158611, 20981092, 12325027, 25388846, 30245029, 33096615) -
Likely benign, no assertion criteria provided	clinical testing	Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	-	- -
Likely benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Likely benign, no assertion criteria provided	clinical testing	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	-	- -
Likely benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 31, 2024	- -
Likely benign, criteria provided, single submitter	clinical testing	Athena Diagnostics	Feb 18, 2019	- -

Autosomal recessive nonsyndromic hearing loss 1A Benign:3

Likely benign, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Apr 27, 2017	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 allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. -
Benign, no assertion criteria provided	clinical testing	Natera, Inc.	Apr 19, 2020	- -
Likely benign, criteria provided, single submitter	clinical testing	Genomic Diagnostic Laboratory, Division of Genomic Diagnostics, Children's Hospital of Philadelphia	May 09, 2017	- -

not specified Benign:2

Benign, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Jun 26, 2012	Phe83Leu in exon 2 of GJB2: This variant is not expected to have clinical signif icance because it has been identified in 0.3% (28/8572) of European American chr omosomes and 0.07% (3/4403) of African American chromosomes from a broad populat ion by the NHLBI Exome sequencing project (http://evs.gs.washington.edu/EVS/; db SNP rs111033218). In addition, this has been observed at equal frequencies in af fected individuals and controls (Scott 1998, Heathcote 2000, Prasad 2000, Rabion et 2000, Pandya 2003, Bruzzone 2003, Frei 2004, Roux 2004, Sinnathuray 2004, Che ng 2005, Santos 2005, Frei 2006, Tang 2006, Ramsebner 2007, Ross 2007, Picotti 2 009, Lee 2009, Kimani 2010). Furthermore, functional studies revealed that the v ariant protein behaves similar to that of the wild type protein (Bruzzone 2003). -
Benign, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	Feb 11, 2015	- -

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

Likely benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Apr 27, 2017

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 allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. -

Nonsyndromic genetic hearing loss Benign:1

Likely benign, criteria provided, single submitter

clinical testing

INGEBI, INGEBI / CONICET

Aug 31, 2020

Based on ACMG/AMP guidelines and Hearing Loss Expert Panel specific criteria: the filtering allele frequency of c.249C>G variant (p.Phe83Leu) in GJB2 gene is 0,28% (404/ 29116 European non-Finnish chromosomes with 95% CI) from Genome Aggregation Database (http://gnomad.broadinstitute.org; calculated by using inverse allele frequency at https://www.cardiodb.org/allelefrequencyapp/), which meets the allele frequency threshold defined by the ClinGen Hearing Loss Expert Panel for considering supporting evidence against pathogenicity for autosomal recessive hearing loss variants (BS1_Supporting). The p.Phe83Leu change has been identified in trans with a pathogenic dominant variant in a family case with KID syndrome applying to BP2 rule (PMID: 10633135). Functional studies demonstrated that p.Phe83Leu mutant generated electrical conductance like the wild type in Xenopus laevis oocytes. Besides, 100% of dye transfer was detected in HeLa cells expressing p.Phe83Leu mutant (PMID:12505163). Hence, this evidence meets BS3_Sup standard. Therefore, this variant meets criteria to be classified as likely benign for autosomal recessive non-syndromic hearing loss: (BS1_Supporting, BP2 and BS3_Supporting). -

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 Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Fulgent Genetics, Fulgent Genetics

Nov 01, 2021

- -

GJB2-related disorder Benign:1

Likely benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Feb 28, 2020

This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Autosomal dominant nonsyndromic hearing loss 3A Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Apr 27, 2017

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 allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.79
BayesDel_addAF	Benign	-0.28	T
BayesDel_noAF	Benign	-0.17
CADD	Benign	0.039
DANN	Benign	0.93
DEOGEN2	Uncertain	0.67	D;D;D
Eigen	Benign	-1.2
Eigen_PC	Benign	-1.2
FATHMM_MKL	Benign	0.16	N
LIST_S2	Benign	0.85	.;.;T
M_CAP	Pathogenic	0.69	D
MetaRNN	Benign	0.033	T;T;T
MetaSVM	Uncertain	-0.24	T
MutationAssessor	Benign	0.29	N;N;N
PrimateAI	Pathogenic	0.80	T
PROVEAN	Benign	-1.3	N;N;.
REVEL	Uncertain	0.42
Sift	Benign	0.35	T;T;.
Sift4G	Benign	0.22	T;T;.
Polyphen		0.0010	B;B;B
Vest4		0.23
MutPred		0.29		Gain of helix (P = 0.132);Gain of helix (P = 0.132);Gain of helix (P = 0.132);
MVP		0.34
MPC		0.051
ClinPred		0.0094	T
GERP RS		-5.8
Varity_R		0.40
gMVP		0.92

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs111033218; hg19: chr13-20763472;