Genetic Variant GJB3:p.Arg32Trp (chr1-34784856-C-T) – ACMG Classification: Benign (-18 pts)

Variant summary

Our verdict is Benign. The variant received -18 ACMG points: 2P and 20B. PM1BP4_StrongBP6_Very_StrongBS1BS2

The NM_024009.3(GJB3):c.94C>T(p.Arg32Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0289 in 1,614,166 control chromosomes in the GnomAD database, including 759 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.021 ( 51 hom., cov: 32)

Exomes 𝑓: 0.030 ( 708 hom. )

Consequence

GJB3
NM_024009.3 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:12

Conservation

PhyloP100: 1.13

Publications

34 publications found

Variant links:

Genes affected

GJB3 (HGNC:4285): (gap junction protein beta 3) This gene is a member of the connexin gene family. The encoded protein is a component of gap junctions, which are composed of arrays of intercellular channels that provide a route for the diffusion of low molecular weight materials from cell to cell. Mutations in this gene can cause non-syndromic deafness or erythrokeratodermia variabilis, a skin disorder. Alternative splicing results in multiple transcript variants encoding the same protein. [provided by RefSeq, Jul 2008]

GJB3 links:

SMIM12 (HGNC:25154): (small integral membrane protein 12) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

SMIM12 links:

ENSG00000255811 (HGNC:):

ENSG00000255811 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -18 ACMG points.

PM1

In a hotspot region, there are 2 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 1 benign, 4 uncertain in NM_024009.3

BP4

Computational evidence support a benign effect (MetaRNN=0.010469735).

BP6

Variant 1-34784856-C-T is Benign according to our data. Variant chr1-34784856-C-T is described in ClinVar as Benign. ClinVar VariationId is 46088.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS1

Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0212 (3221/152286) while in subpopulation NFE AF = 0.0311 (2117/68024). AF 95% confidence interval is 0.03. There are 51 homozygotes in GnomAd4. There are 1605 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.

BS2

High Homozygotes in GnomAd4 at 51 AR,AD,Unknown gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024009.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GJB3	NM_024009.3	MANE Select	c.94C>T	p.Arg32Trp	missense	Exon 2 of 2	NP_076872.1	O75712
	GJB3	NM_001005752.2		c.94C>T	p.Arg32Trp	missense	Exon 2 of 2	NP_001005752.1	O75712

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
GJB3	ENST00000373366.3	TSL:1 MANE Select	c.94C>T	p.Arg32Trp	missense	Exon 2 of 2	ENSP00000362464.2	O75712
GJB3	ENST00000373362.3	TSL:1	c.94C>T	p.Arg32Trp	missense	Exon 2 of 2	ENSP00000362460.3	O75712
SMIM12	ENST00000426886.1	TSL:1	n.208-66447G>A		intron	N/A	ENSP00000429902.1	E5RH51

Frequencies

GnomAD3 genomes

AF:

0.0212

AC:

3224

AN:

152168

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00507

Gnomad AMI

AF:

0.00110

Gnomad AMR

AF:

0.0118

Gnomad ASJ

AF:

0.0156

Gnomad EAS

AF:

0.000577

Gnomad SAS

AF:

0.0104

Gnomad FIN

AF:

0.0547

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.0311

Gnomad OTH

AF:

0.0130

GnomAD2 exomes

AF:

0.0234

AC:

5877

AN:

251420

AF XY:

0.0239

show subpopulations

Gnomad AFR exome

AF:

0.00548

Gnomad AMR exome

AF:

0.00734

Gnomad ASJ exome

AF:

0.0149

Gnomad EAS exome

AF:

0.0000544

Gnomad FIN exome

AF:

0.0532

Gnomad NFE exome

AF:

0.0326

Gnomad OTH exome

AF:

0.0201

GnomAD4 exome

AF:

0.0297

AC:

43378

AN:

1461880

Hom.:

708

Cov.:

AF XY:

0.0293

AC XY:

21333

AN XY:

727236

show subpopulations

African (AFR)

AF:

0.00445

AC:

149

AN:

33480

American (AMR)

AF:

0.00818

AC:

366

AN:

44722

Ashkenazi Jewish (ASJ)

AF:

0.0149

AC:

390

AN:

26136

East Asian (EAS)

AF:

0.000101

AC:

AN:

39700

South Asian (SAS)

AF:

0.0128

AC:

1108

AN:

86258

European-Finnish (FIN)

AF:

0.0542

AC:

2897

AN:

53420

Middle Eastern (MID)

AF:

0.00347

AC:

AN:

5768

European-Non Finnish (NFE)

AF:

0.0332

AC:

36945

AN:

1112000

Other (OTH)

AF:

0.0248

AC:

1499

AN:

60396

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.478

Heterozygous variant carriers

2680

5361

8041

10722

13402

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1372

2744

4116

5488

6860

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0212

AC:

3221

AN:

152286

Hom.:

Cov.:

AF XY:

0.0216

AC XY:

1605

AN XY:

74450

show subpopulations

African (AFR)

AF:

0.00505

AC:

210

AN:

41556

American (AMR)

AF:

0.0118

AC:

180

AN:

15302

Ashkenazi Jewish (ASJ)

AF:

0.0156

AC:

AN:

3470

East Asian (EAS)

AF:

0.000578

AC:

AN:

5190

South Asian (SAS)

AF:

0.00995

AC:

AN:

4826

European-Finnish (FIN)

AF:

0.0547

AC:

580

AN:

10606

Middle Eastern (MID)

AF:

0.00340

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0311

AC:

2117

AN:

68024

Other (OTH)

AF:

0.0128

AC:

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

160

321

481

642

802

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

120

160

200

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0275

Hom.:

168

Bravo

AF:

0.0171

TwinsUK

AF:

0.0316

AC:

117

ALSPAC

AF:

0.0368

AC:

142

ESP6500AA

AF:

0.00817

AC:

ESP6500EA

AF:

0.0307

AC:

264

ExAC

AF:

0.0242

AC:

2939

Asia WGS

AF:

0.00549

AC:

AN:

3478

EpiCase

AF:

0.0262

EpiControl

AF:

0.0245

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, multiple submitters, no conflicts

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (6)

not specified (5)

Erythrokeratodermia variabilis et progressiva 1 (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Pathogenic

0.88

BayesDel_addAF

Benign

-0.13

BayesDel_noAF

Uncertain

0.060

CADD

Uncertain

(source)

DANN

Pathogenic

1.0

DEOGEN2

Pathogenic

0.95

Eigen

Pathogenic

0.72

Eigen_PC

Uncertain

0.59

FATHMM_MKL

Uncertain

0.85

LIST_S2

Uncertain

0.95

MetaRNN

Benign

0.010

MetaSVM

Uncertain

0.47

MutationAssessor

Pathogenic

4.0

PhyloP100

1.1

PrimateAI

Uncertain

0.72

PROVEAN

Pathogenic

-7.0

REVEL

Pathogenic

0.68

Sift

Pathogenic

0.0

Sift4G

Pathogenic

0.0010

Polyphen

1.0

Vest4

0.23

MPC

0.40

ClinPred

0.072

GERP RS

5.8

Varity_R

0.83

gMVP

0.96

Mutation Taster

=93/7

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over