rs2070776

Positions:

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_000626.4(CD79B):c.366T>C(p.Cys122=) 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:4O:1

Conservation

PhyloP100: 0.0680

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 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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 id is 402520.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-63930138-A-G is described in Lovd as [Benign].

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/exons	MANE
CD79B	NM_000626.4 linkuse as main transcript	c.366T>C	p.Cys122=	synonymous_variant	3/6	ENST00000006750.8
CD79B	NM_001039933.3 linkuse as main transcript	c.369T>C	p.Cys123=	synonymous_variant	3/6
CD79B	NM_001329050.2 linkuse as main transcript	c.122-250T>C		intron_variant
CD79B	NM_021602.4 linkuse as main transcript	c.119-250T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CD79B	ENST00000006750.8 linkuse as main transcript	c.366T>C	p.Cys122=	synonymous_variant	3/6	1	NM_000626.4	P4	P40259-1

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

GnomAD3 exomes

AF:

0.589

AC:

147820

AN:

250870

Hom.:

44526

AF XY:

0.589

AC XY:

79886

AN XY:

135648

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 SAS exome

AF:

0.455

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

Gnomad4 AFR exome

AF:

0.673

Gnomad4 AMR exome

AF:

0.500

Gnomad4 ASJ exome

AF:

0.672

Gnomad4 EAS exome

AF:

0.462

Gnomad4 SAS exome

AF:

0.462

Gnomad4 FIN exome

AF:

0.588

Gnomad4 NFE exome

AF:

0.653

Gnomad4 OTH exome

AF:

0.618

GnomAD4 genome

AF:

0.633

AC:

96249

AN:

152126

Hom.:

30762

Cov.:

AF XY:

0.622

AC XY:

46271

AN XY:

74346

show subpopulations

Gnomad4 AFR

AF:

0.672

Gnomad4 AMR

AF:

0.531

Gnomad4 ASJ

AF:

0.664

Gnomad4 EAS

AF:

0.461

Gnomad4 SAS

AF:

0.440

Gnomad4 FIN

AF:

0.585

Gnomad4 NFE

AF:

0.662

Gnomad4 OTH

AF:

0.630

Alfa

AF:

0.653

Hom.:

51344

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:4Other:1

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:2

Benign, criteria provided, single submitter	clinical testing	Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan	Jan 24, 2024	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. -
Benign, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Mar 28, 2016	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 -

not provided

Benign:1Other:1

Benign, criteria provided, single submitter	clinical testing	GeneDx	Nov 10, 2018	- -
not provided, no classification provided	phenotyping only	GenomeConnect, ClinGen	-	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. -

Agammaglobulinemia 6, autosomal recessive

Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Feb 01, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

DANN

Benign

0.50

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over