rs367608135

Variant names:

• chr19-41880705-C-A
• rs367608135
• NM_001783.4:c.534C>A

Your query was ambiguous. Multiple possible variants found:

• chr19-41880705-C-A
• chr19-41880705-C-T

Variant summary

Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2 BP4_Strong BP7

The NM_001783.4(CD79A):​c.534C>A​(p.Ala178Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000866 in 1,154,924 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. A178A) has been classified as Likely benign.

• Frequency:
  • Genomes: not found (cov: 28)
  • Exomes 𝑓: 8.7e-7 (0 hom.)
• Consequence: CD79A NM_001783.4 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.179
• Publications: 0 publications found

Genes affected

CD79A (HGNC:1698): (CD79a 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-alpha protein of the B-cell antigen component. Alternatively spliced transcript variants encoding different isoforms have been described. [provided by RefSeq, Jul 2008]

CD79A Gene-Disease associations (from GenCC):

• agammaglobulinemia 3, autosomal recessive

  Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics, ClinGen
• autosomal agammaglobulinemia

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Likely_benign. The variant received -3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BP7: Synonymous conserved (PhyloP=-0.179 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CD79A	NM_001783.4	c.534C>A	p.Ala178Ala	synonymous_variant	Exon 4 of 5	ENST00000221972.8	NP_001774.1
CD79A	NM_021601.4	c.420C>A	p.Ala140Ala	synonymous_variant	Exon 4 of 5		NP_067612.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CD79A	ENST00000221972.8	c.534C>A	p.Ala178Ala	synonymous_variant	Exon 4 of 5	1	NM_001783.4	ENSP00000221972.3
CD79A	ENST00000444740.2	c.420C>A	p.Ala140Ala	synonymous_variant	Exon 4 of 5	1		ENSP00000400605.1
CD79A	ENST00000597454.2	c.779C>A	p.Pro260Gln	missense_variant	Exon 3 of 4	3		ENSP00000468922.2

Frequencies

GnomAD3 genomes Cov.: 28

GnomAD4 exome AF: 8.66e-7 AC: 1 AN: 1154924 Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0 AN XY: 566386

African (AFR) AF: 0.00 AC: 0 AN: 24504

American (AMR) AF: 0.00 AC: 0 AN: 28344

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 15974

East Asian (EAS) AF: 0.00 AC: 0 AN: 13094

South Asian (SAS) AF: 0.00 AC: 0 AN: 77032

European-Finnish (FIN) AF: 0.0000350 AC: 1 AN: 28542

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4186

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 921544

Other (OTH) AF: 0.00 AC: 0 AN: 41704

GnomAD4 genome Cov.: 28

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	4.2
DANN	Benign	0.67
PhyloP100		-0.18
Mutation Taster		=100/0	polymorphism

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

Other links and lift over

dbSNP: rs367608135; hg19: chr19-42384772;