rs2070776

Variant names:

• chr17-63930138-A-G
• rs2070776
• NM_000626.4:c.366T>C

Your query was ambiguous. Multiple possible variants found:

• chr17-63930138-A-G
• chr17-63930138-A-C
• chr17-63930138-A-T

Variant summary

Our verdict is Benign. The variant received -21 ACMG points: 0P and 21B. BP4_Strong BP6_Very_Strong BP7 BA1

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
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:5 O:1
• Conservation: PhyloP100: 0.0680
• Publications: 68 publications found

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: ClinGen, Labcorp Genetics (formerly Invitae), Ambry Genetics
• autosomal agammaglobulinemia

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

ENSG00000285947 (HGNC:):

ACMG classification

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000626.4. 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
	CD79B	NM_000626.4	MANE Select	c.366T>C	p.Cys122Cys	synonymous	Exon 3 of 6	NP_000617.1	P40259-1
	CD79B	NM_001039933.3		c.369T>C	p.Cys123Cys	synonymous	Exon 3 of 6	NP_001035022.1	P40259-3
	CD79B	NM_001329050.2		c.122-250T>C		intron	N/A	NP_001315979.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD79B	ENST00000006750.8	TSL:1 MANE Select	c.366T>C	p.Cys122Cys	synonymous	Exon 3 of 6	ENSP00000006750.4	P40259-1
	CD79B	ENST00000392795.7	TSL:1	c.369T>C	p.Cys123Cys	synonymous	Exon 3 of 6	ENSP00000376544.3	P40259-3
	ENSG00000285947	ENST00000647774.1		c.50-250T>C		intron	N/A	ENSP00000497443.1	A0A3B3ISS9

Frequencies

GnomAD3 genomes AF: 0.633 AC: 96193 AN: 152008 Hom.: 30746 Cov.: 32

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

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.: 54 AF XY: 0.626 AC XY: 454920 AN XY: 727082

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

GnomAD4 genome AF: 0.633 AC: 96249 AN: 152126 Hom.: 30762 Cov.: 32 AF XY: 0.622 AC XY: 46271 AN XY: 74346

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

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

ClinVar submissions

Significance: Benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	2	not provided (3)
-	-	2	not specified (2)
-	-	1	Agammaglobulinemia 6, autosomal recessive (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	11
DANN	Benign	0.50
PhyloP100		0.068
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2070776; hg19: chr17-62007498; COSMIC: COSV50075913; COSMIC: COSV50075913;