chr17-63930138-A-G

Variant names:

Variant summary

Our verdict is Benign. The variant received -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_000626.4(CD79B):c.366T>C(p.Cys122Cys) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.63 in 1,613,682 control chromosomes in the GnomAD database, including 323,233 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.63 ( 30762 hom., cov: 32)

Exomes 𝑓: 0.63 ( 292471 hom. )

Consequence

CD79B
NM_000626.4 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:5O:1

Conservation

PhyloP100: 0.0680

Publications

68 publications found

Variant links:

Genes affected

CD79B (HGNC:1699): (CD79b molecule) The B lymphocyte antigen receptor is a multimeric complex that includes the antigen-specific component, surface immunoglobulin (Ig). Surface Ig non-covalently associates with two other proteins, Ig-alpha and Ig-beta, which are necessary for expression and function of the B-cell antigen receptor. This gene encodes the Ig-beta protein of the B-cell antigen component. Alternatively spliced transcript variants encoding different isoforms have been described. [provided by RefSeq, Jul 2008]

CD79B Gene-Disease associations (from GenCC):

agammaglobulinemia 6, autosomal recessive
Inheritance: AR Classification: DEFINITIVE, STRONG, MODERATE Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae), ClinGen
autosomal agammaglobulinemia
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

CD79B links:

ENSG00000285947 (HGNC:):

ENSG00000285947 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BP6

Variant 17-63930138-A-G is Benign according to our data. Variant chr17-63930138-A-G is described in ClinVar as Benign. ClinVar VariationId is 402520.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=0.068 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.666 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CD79B	NM_000626.4 link	c.366T>C	p.Cys122Cys	synonymous_variant	Exon 3 of 6	ENST00000006750.8	NP_000617.1	P40259-1
CD79B	NM_001039933.3 link	c.369T>C	p.Cys123Cys	synonymous_variant	Exon 3 of 6		NP_001035022.1	P40259-3
CD79B	NM_001329050.2 link	c.122-250T>C		intron_variant	Intron 2 of 4		NP_001315979.1
CD79B	NM_021602.4 link	c.119-250T>C		intron_variant	Intron 2 of 4		NP_067613.1	P40259-2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CD79B	ENST00000006750.8 link	c.366T>C	p.Cys122Cys	synonymous_variant	Exon 3 of 6	1	NM_000626.4	ENSP00000006750.4		P40259-1
ENSG00000285947	ENST00000647774.1 link	c.50-250T>C		intron_variant	Intron 1 of 7			ENSP00000497443.1		A0A3B3ISS9

Frequencies

GnomAD3 genomes

AF:

0.633

AC:

96193

AN:

152008

Hom.:

30746

Cov.:

show subpopulations

Gnomad AFR

AF:

0.672

Gnomad AMI

AF:

0.765

Gnomad AMR

AF:

0.531

Gnomad ASJ

AF:

0.664

Gnomad EAS

AF:

0.462

Gnomad SAS

AF:

0.441

Gnomad FIN

AF:

0.585

Gnomad MID

AF:

0.734

Gnomad NFE

AF:

0.662

Gnomad OTH

AF:

0.630

GnomAD2 exomes

AF:

0.589

AC:

147820

AN:

250870

AF XY:

0.589

show subpopulations

Gnomad AFR exome

AF:

0.672

Gnomad AMR exome

AF:

0.494

Gnomad ASJ exome

AF:

0.668

Gnomad EAS exome

AF:

0.459

Gnomad FIN exome

AF:

0.585

Gnomad NFE exome

AF:

0.656

Gnomad OTH exome

AF:

0.612

GnomAD4 exome

AF:

0.629

AC:

919667

AN:

1461556

Hom.:

292471

Cov.:

AF XY:

0.626

AC XY:

454920

AN XY:

727082

show subpopulations

African (AFR)

AF:

0.673

AC:

22525

AN:

33478

American (AMR)

AF:

0.500

AC:

22328

AN:

44688

Ashkenazi Jewish (ASJ)

AF:

0.672

AC:

17557

AN:

26134

East Asian (EAS)

AF:

0.462

AC:

18351

AN:

39688

South Asian (SAS)

AF:

0.462

AC:

39808

AN:

86248

European-Finnish (FIN)

AF:

0.588

AC:

31369

AN:

53372

Middle Eastern (MID)

AF:

0.694

AC:

4003

AN:

5766

European-Non Finnish (NFE)

AF:

0.653

AC:

726391

AN:

1111794

Other (OTH)

AF:

0.618

AC:

37335

AN:

60388

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.484

Heterozygous variant carriers

20920

41839

62759

83678

104598

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

18864

37728

56592

75456

94320

<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:

0.633

AC:

96249

AN:

152126

Hom.:

30762

Cov.:

AF XY:

0.622

AC XY:

46271

AN XY:

74346

show subpopulations

African (AFR)

AF:

0.672

AC:

27904

AN:

41510

American (AMR)

AF:

0.531

AC:

8122

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.664

AC:

2303

AN:

3470

East Asian (EAS)

AF:

0.461

AC:

2383

AN:

5164

South Asian (SAS)

AF:

0.440

AC:

2121

AN:

4820

European-Finnish (FIN)

AF:

0.585

AC:

6191

AN:

10580

Middle Eastern (MID)

AF:

0.731

AC:

215

AN:

294

European-Non Finnish (NFE)

AF:

0.662

AC:

44980

AN:

67968

Other (OTH)

AF:

0.630

AC:

1334

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1853

3706

5560

7413

9266

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

780

1560

2340

3120

3900

<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:

0.651

Hom.:

110762

Bravo

AF:

0.632

Asia WGS

AF:

0.462

AC:

1610

AN:

3478

EpiCase

AF:

0.667

EpiControl

AF:

0.665

ClinVar

Significance: Benign

Submissions summary: Benign:5Other:1

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2Other:1

Nov 10, 2018

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

GenomeConnect, ClinGen

Significance:not provided

Review Status:no classification provided

Collection Method:phenotyping only

Variant interpreted as Benign and reported on 04-27-2020 by Lab or GTR ID 500031. GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant. This variant was reported in an individual referred for clinical diagnostic genetic testing. -

Breakthrough Genomics, Breakthrough Genomics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:not provided

- -

not specified

Benign:2

Jan 24, 2024

Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

This variant is classified as Benign based on local population frequency. This variant was detected in 82% of patients studied by a panel of primary immunodeficiencies. Number of patients: 78. Only high quality variants are reported. -

Mar 28, 2016

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -

Agammaglobulinemia 6, autosomal recessive

Benign:1

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

(source)

DANN

Benign

0.50

PhyloP100

0.068

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over