19-41878977-T-C

Variant names:

• chr19-41878977-T-C
• rs2074204310
• NM_001783.4:c.80-13T>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.80-13T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000794 in 503,932 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.

• Frequency:
  • Genomes: not found (cov: 31)
  • Exomes 𝑓: 0.0000079 (0 hom.)
• Consequence: CD79A NM_001783.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03
• 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 -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CD79A	NM_001783.4	c.80-13T>C		intron_variant	Intron 1 of 4	ENST00000221972.8	NP_001774.1
CD79A	NM_021601.4	c.80-13T>C		intron_variant	Intron 1 of 4		NP_067612.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CD79A	ENST00000221972.8	c.80-13T>C		intron_variant	Intron 1 of 4	1	NM_001783.4	ENSP00000221972.3
CD79A	ENST00000444740.2	c.80-13T>C		intron_variant	Intron 1 of 4	1		ENSP00000400605.1
CD79A	ENST00000597454.2	c.80-13T>C		intron_variant	Intron 1 of 3	3		ENSP00000468922.2

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome AF: 0.00000794 AC: 4 AN: 503932 Hom.: 0 Cov.: 13 AF XY: 0.00000364 AC XY: 1 AN XY: 274976

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.00 AC: 0 AN: 13672

American (AMR) AF: 0.00 AC: 0 AN: 37754

Ashkenazi Jewish (ASJ) AF: 0.0000688 AC: 1 AN: 14528

East Asian (EAS) AF: 0.00 AC: 0 AN: 19014

South Asian (SAS) AF: 0.00 AC: 0 AN: 68870

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 29864

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3280

European-Non Finnish (NFE) AF: 0.0000102 AC: 3 AN: 294232

Other (OTH) AF: 0.00 AC: 0 AN: 22718

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0.000000), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.76
DANN	Benign	0.40
PhyloP100		-1.0

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: rs2074204310; hg19: chr19-42383047;