19-41881402-G-A

Position:

• chr19-41881402-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The 19-41881402-G-A variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.51 in 342,696 control chromosomes in the GnomAD database, including 47,642 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.47 (18396 hom., cov: 31)
  • Exomes 𝑓: 0.54 (29246 hom.)
• Consequence: CD79A NM_001783.4 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.165

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 Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.565 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CD79A	NM_001783.4			downstream_gene_variant		ENST00000221972.8	NP_001774.1
CD79A	NM_021601.4			downstream_gene_variant			NP_067612.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CD79A	ENST00000221972.8			downstream_gene_variant		1	NM_001783.4	ENSP00000221972	P1

Frequencies

GnomAD3 genomes AF: 0.469 AC: 71188 AN: 151702 Hom.: 18393 Cov.: 31

Gnomad AFR AF: 0.230

Gnomad AMI AF: 0.694

Gnomad AMR AF: 0.531

Gnomad ASJ AF: 0.638

Gnomad EAS AF: 0.475

Gnomad SAS AF: 0.584

Gnomad FIN AF: 0.570

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.563

Gnomad OTH AF: 0.517

GnomAD4 exome AF: 0.542 AC: 103466 AN: 190876 Hom.: 29246 Cov.: 0 AF XY: 0.547 AC XY: 52660 AN XY: 96254

Gnomad4 AFR exome AF: 0.227

Gnomad4 AMR exome AF: 0.528

Gnomad4 ASJ exome AF: 0.644

Gnomad4 EAS exome AF: 0.474

Gnomad4 SAS exome AF: 0.590

Gnomad4 FIN exome AF: 0.554

Gnomad4 NFE exome AF: 0.559

Gnomad4 OTH exome AF: 0.541

GnomAD4 genome AF: 0.469 AC: 71199 AN: 151820 Hom.: 18396 Cov.: 31 AF XY: 0.473 AC XY: 35103 AN XY: 74180

Gnomad4 AFR AF: 0.230

Gnomad4 AMR AF: 0.531

Gnomad4 ASJ AF: 0.638

Gnomad4 EAS AF: 0.476

Gnomad4 SAS AF: 0.583

Gnomad4 FIN AF: 0.570

Gnomad4 NFE AF: 0.563

Gnomad4 OTH AF: 0.511

Alfa AF: 0.535 Hom.: 14546

Bravo AF: 0.453

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.9

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs3810153; hg19: chr19-42385469;