rs367608135

chr19-41880705-C-T

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2 BP4_Strong BP6_Moderate BP7

The NM_001783.4(CD79A):c.534C>T(p.Ala178=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000204 in 1,295,016 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.00098 (0 hom., cov: 28)
  • Exomes 𝑓: 0.00011 (0 hom.)
• Consequence: CD79A NM_001783.4 synonymous
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.179

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]

ACMG classification

Verdict is Likely_benign. Variant got -5 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BP6: Variant 19-41880705-C-T is Benign according to our data. Variant chr19-41880705-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 487217.Status of the report is criteria_provided_single_submitter, 1 stars.
• BP7: Synonymous conserved (PhyloP=-0.179 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CD79A	NM_001783.4	c.534C>T	p.Ala178=	synonymous_variant	4/5	ENST00000221972.8
CD79A	NM_021601.4	c.420C>T	p.Ala140=	synonymous_variant	4/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CD79A	ENST00000221972.8	c.534C>T	p.Ala178=	synonymous_variant	4/5	1	NM_001783.4	P1
CD79A	ENST00000444740.2	c.420C>T	p.Ala140=	synonymous_variant	4/5	1
CD79A	ENST00000597454.2	c.779C>T	p.Pro260Leu	missense_variant	3/4	3

Frequencies

GnomAD3 genomes AF: 0.000986 AC: 138 AN: 139954 Hom.: 0 Cov.: 28

Gnomad AFR AF: 0.00317

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000632

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000541

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000157

Gnomad OTH AF: 0.00101

GnomAD3 exomes AF: 0.000193 AC: 30 AN: 155430 Hom.: 0 AF XY: 0.000183 AC XY: 15 AN XY: 82110

Gnomad AFR exome AF: 0.00237

Gnomad AMR exome AF: 0.000203

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.000132

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000167

Gnomad OTH exome AF: 0.000228

GnomAD4 exome AF: 0.000110 AC: 127 AN: 1154922 Hom.: 0 Cov.: 33 AF XY: 0.0000865 AC XY: 49 AN XY: 566386

Gnomad4 AFR exome AF: 0.00388

Gnomad4 AMR exome AF: 0.000212

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.0000764

Gnomad4 SAS exome AF: 0.0000389

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000977

Gnomad4 OTH exome AF: 0.000312

GnomAD4 genome AF: 0.000978 AC: 137 AN: 140094 Hom.: 0 Cov.: 28 AF XY: 0.00115 AC XY: 78 AN XY: 67926

Gnomad4 AFR AF: 0.00314

Gnomad4 AMR AF: 0.000631

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000538

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000157

Gnomad4 OTH AF: 0.000995

Alfa AF: 0.000498 Hom.: 0

Asia WGS AF: 0.000289 AC: 1 AN: 3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Agammaglobulinemia 3, autosomal recessive Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Invitae

Jan 01, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
Cadd	Benign	8.6
Dann	Benign	0.62

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

LitVar

Other links and lift over

dbSNP: rs367608135; hg19: chr19-42384772;