19-41881402-G-C

Variant names:

• chr19-41881402-G-C
• rs3810153
• NM_001783.4:c.*422G>C

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001783.4(CD79A):​c.*422G>C variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 31)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: CD79A NM_001783.4 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.165
• Publications: 10 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: ClinGen, Labcorp Genetics (formerly Invitae), Ambry Genetics
• autosomal agammaglobulinemia

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001783.4. 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
	CD79A	NM_001783.4	MANE Select	c.*422G>C		downstream_gene	N/A	NP_001774.1	P11912-1
	CD79A	NM_021601.4		c.*422G>C		downstream_gene	N/A	NP_067612.1	P11912-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD79A	ENST00000221972.8	TSL:1 MANE Select	c.*422G>C		downstream_gene	N/A	ENSP00000221972.3	P11912-1

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 191336 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 96488

African (AFR) AF: 0.00 AC: 0 AN: 8082

American (AMR) AF: 0.00 AC: 0 AN: 8516

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 7644

East Asian (EAS) AF: 0.00 AC: 0 AN: 16924

South Asian (SAS) AF: 0.00 AC: 0 AN: 20226

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 4454

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 894

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 112468

Other (OTH) AF: 0.00 AC: 0 AN: 12128

GnomAD4 genome Cov.: 31

Alfa AF: 0.00 Hom.: 24991

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.3
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs3810153; hg19: chr19-42385469;