rs76983681

Variant names:

• chr19-41878687-G-A
• rs76983681
• NM_001783.4:c.80-303G>A

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_001783.4(CD79A):​c.80-303G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0395 in 152,108 control chromosomes in the GnomAD database, including 338 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.039 (338 hom., cov: 31)
• Consequence: CD79A NM_001783.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -3.91
• 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: Benign. The variant received -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BP6: Variant 19-41878687-G-A is Benign according to our data. Variant chr19-41878687-G-A is described in ClinVar as [Benign]. Clinvar id is 1233380.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.207 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CD79A	NM_001783.4	c.80-303G>A		intron_variant	Intron 1 of 4	ENST00000221972.8	NP_001774.1
CD79A	NM_021601.4	c.80-303G>A		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.80-303G>A		intron_variant	Intron 1 of 4	1	NM_001783.4	ENSP00000221972.3
CD79A	ENST00000444740.2	c.80-303G>A		intron_variant	Intron 1 of 4	1		ENSP00000400605.1
CD79A	ENST00000597454.2	c.80-303G>A		intron_variant	Intron 1 of 3	3		ENSP00000468922.2

Frequencies

GnomAD3 genomes AF: 0.0395 AC: 6001 AN: 151990 Hom.: 341 Cov.: 31

Gnomad AFR AF: 0.0778

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0107

Gnomad ASJ AF: 0.00806

Gnomad EAS AF: 0.219

Gnomad SAS AF: 0.116

Gnomad FIN AF: 0.0542

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.00384

Gnomad OTH AF: 0.0268

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0395 AC: 6006 AN: 152108 Hom.: 338 Cov.: 31 AF XY: 0.0436 AC XY: 3245 AN XY: 74370

African (AFR) AF: 0.0778 AC: 3225 AN: 41474

American (AMR) AF: 0.0107 AC: 164 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.00806 AC: 28 AN: 3472

East Asian (EAS) AF: 0.218 AC: 1124 AN: 5162

South Asian (SAS) AF: 0.116 AC: 560 AN: 4818

European-Finnish (FIN) AF: 0.0542 AC: 574 AN: 10598

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.00381 AC: 259 AN: 67980

Other (OTH) AF: 0.0304 AC: 64 AN: 2108

Alfa AF: 0.0142 Hom.: 31

Bravo AF: 0.0377

Asia WGS AF: 0.171 AC: 594 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Jun 21, 2021

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.27
DANN	Benign	0.68
PhyloP100		-3.9
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.040		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: rs76983681; hg19: chr19-42382757;