rs376898963

chr13-20189089-G-A

Variant summary

Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM1 BP4_Strong BP6

The NM_004004.6(GJB2):c.493C>T(p.Arg165Trp) variant causes a missense change. The variant allele was found at a frequency of 0.000208 in 1,614,022 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

• Frequency:
  • Genomes: 𝑓 0.00014 (0 hom., cov: 33)
  • Exomes 𝑓: 0.00021 (2 hom.)
• Consequence: GJB2 NM_004004.6 missense
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:3 B:9
• Conservation: PhyloP100: 6.68

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 Likely_benign. Variant got -3 ACMG points.

• PM1: In a hotspot region, there are 5 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 1 benign, 8 uncertain in NM_004004.6
• BP4: Computational evidence support a benign effect (MetaRNN=0.019080848).
• BP6: Variant 13-20189089-G-A is Benign according to our data. Variant chr13-20189089-G-A is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 177736.We mark this variant Likely_benign, oryginal submissions are: {Uncertain_significance=3, Likely_benign=8, Benign=1}.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GJB2	NM_004004.6	c.493C>T	p.Arg165Trp	missense_variant	2/2	ENST00000382848.5
GJB2	XM_011535049.3	c.493C>T	p.Arg165Trp	missense_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GJB2	ENST00000382848.5	c.493C>T	p.Arg165Trp	missense_variant	2/2	1	NM_004004.6	P1
GJB2	ENST00000382844.2	c.493C>T	p.Arg165Trp	missense_variant	1/1			P1

Frequencies

GnomAD3 genomes AF: 0.000158 AC: 24 AN: 152176 Hom.: 1 Cov.: 33

Gnomad AFR AF: 0.000193

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00331

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.000581 AC: 146 AN: 251098 Hom.: 1 AF XY: 0.000648 AC XY: 88 AN XY: 135730

Gnomad AFR exome AF: 0.000185

Gnomad AMR exome AF: 0.000145

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00438

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.000652

GnomAD4 exome AF: 0.000215 AC: 314 AN: 1461728 Hom.: 2 Cov.: 33 AF XY: 0.000263 AC XY: 191 AN XY: 727158

Gnomad4 AFR exome AF: 0.0000597

Gnomad4 AMR exome AF: 0.0000894

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00326

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000450

Gnomad4 OTH exome AF: 0.000364

GnomAD4 genome AF: 0.000144 AC: 22 AN: 152294 Hom.: 0 Cov.: 33 AF XY: 0.000201 AC XY: 15 AN XY: 74466

Gnomad4 AFR AF: 0.000193

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00290

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00

Gnomad4 OTH AF: 0.00

Bravo AF: 0.0000416

ExAC AF: 0.000659 AC: 80

Asia WGS AF: 0.00115 AC: 4 AN: 3478

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Uncertain:3 Benign:9

Revision: criteria provided, conflicting classifications

Submissions by phenotype

not provided Uncertain:2 Benign:2

Uncertain significance, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	Nov 19, 2014	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Athena Diagnostics	May 17, 2019	- -
Likely benign, criteria provided, single submitter	clinical testing	GeneDx	Mar 05, 2021	Observed as heterozygous variant without a second pathogenic variant in multiple individuals with hearing loss but also in unaffected relatives in published literature (Rickard et al., 2001; Putcha et al., 2007; Vanniya et al., 2017; Gurtler et al., 2008; Amritkumar et al., 2018); Located in the second extracellular domain of Cx26; In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; This variant is associated with the following publications: (PMID: 32425985, 31992338, 30245029, 20863150, 29542069, 29148562, 16950989, 12746422, 20234132, 17666888, 18607988, 20086306, 18941476, 29921236, 25388846, 11494963, 15617550) -
Likely benign, criteria provided, single submitter	clinical testing	Invitae	Jan 29, 2024	- -

Autosomal recessive nonsyndromic hearing loss 1A Uncertain:1 Benign:3

Likely benign, criteria provided, single submitter	clinical testing	Pars Genome Lab	May 18, 2021	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Counsyl	Jul 14, 2017	- -
Benign, criteria provided, single submitter	clinical testing	Mendelics	May 28, 2019	- -
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). 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 determine this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. -

not specified Benign:2

Likely benign, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	May 02, 2018	Variant summary: GJB2 c.493C>T (p.Arg165Trp) results in a non-conservative amino acid change located in the cysteine-rich domain (IPR019570) of the encoded protein sequence. Three of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 0.00066 in 121246 control chromosomes (ExAC), predominantly observed within the South Asian subpopulation at a frequency of 0.0046, including 2 homozygotes. This frequency is not significantly higher than expected for a pathogenic variant in GJB2 causing Autosomal Recessive Non-Syndromic Hearing Loss (0.00066 vs 0.025), allowing no conclusion about variant significance. The variant, c.493C>T, has been reported in the literature in individuals affected with Non-Syndromic Hearing Loss (NSHL) (Rickard 2001, Gurtler 2008, RamShankar 2003, Hamid 2009), however in none of these cases was a second allele identified. In addition, Santos_2005, reports two families in which affected individuals do not carry the variant of interest, showing lack of cosegregation. At least one publication reported experimental evidence evaluating an impact on protein function, demonstrating the constriction of the channel pore in an intercellular dye transfer experiment (Xiao 2011). This defect might prevent the transmission of biochemically active molecules between cells, however, its implication in the pathomechanism is currently not clarified, and therefore this result does not allow convincing conclusions about the variant effect. A ClinVar submission from a clinical diagnostic laboratory (evaluation after 2014) cites the variant as "likely benign." Based on the evidence outlined above, the variant was classified as likely benign. -
Likely benign, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Dec 06, 2014	p.Arg165Trp in exon 2 of GJB2: This variant has been identified in 7 individuals with hearing loss (Rickard 2001, Putcha 2007, Santos 2005); however several of these individuals did not carry a second GJB2 variant. This variant is not expec ted to have clinical significance because it is has been identified in 0.4% (77/ 16,586) of South Asian chromosomes by the Exome Aggregation Consortium (http://e xac.broadinstitute.org/;dbSNP rs376898963). -

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. -

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	Benign	0.30
BayesDel_addAF	Uncertain	0.16	D
BayesDel_noAF	Pathogenic	0.46
Cadd	Uncertain	26
Dann	Uncertain	1.0
DEOGEN2	Pathogenic	0.88	D;D;D
Eigen	Uncertain	0.56
Eigen_PC	Uncertain	0.61
FATHMM_MKL	Uncertain	0.97	D
M_CAP	Uncertain	0.13	D
MetaRNN	Benign	0.019	T;T;T
MetaSVM	Uncertain	0.69	D
MutationAssessor	Pathogenic	3.1	M;M;M
MutationTaster	Benign	1.0	D;D
PrimateAI	Uncertain	0.68	T
PROVEAN	Pathogenic	-5.4	D;D;.
REVEL	Pathogenic	0.83
Sift	Benign	0.23	T;T;.
Sift4G	Benign	0.13	T;T;.
Polyphen		0.92	P;P;P
Vest4		0.92
MutPred		0.72		Gain of ubiquitination at K168 (P = 0.0851);Gain of ubiquitination at K168 (P = 0.0851);Gain of ubiquitination at K168 (P = 0.0851);
MVP		0.96
MPC		0.049
ClinPred		0.17	T
GERP RS		5.5
Varity_R		0.64
gMVP		0.90

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: rs376898963; hg19: chr13-20763228;