19-41878687-G-A

Variant summary

Our verdict is Benign. Variant got -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

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 -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/exons	MANE	UniProt
CD79A	NM_001783.4	c.80-303G>A		intron_variant		ENST00000221972.8
CD79A	NM_021601.4	c.80-303G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CD79A	ENST00000221972.8	c.80-303G>A		intron_variant		1	NM_001783.4	P1
CD79A	ENST00000444740.2	c.80-303G>A		intron_variant		1
CD79A	ENST00000597454.2	c.80-303G>A		intron_variant		3

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

Gnomad4 AFR AF: 0.0778

Gnomad4 AMR AF: 0.0107

Gnomad4 ASJ AF: 0.00806

Gnomad4 EAS AF: 0.218

Gnomad4 SAS AF: 0.116

Gnomad4 FIN AF: 0.0542

Gnomad4 NFE AF: 0.00381

Gnomad4 OTH AF: 0.0304

Alfa AF: 0.0158 Hom.: 17

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

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 21, 2021

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.27
Dann	Benign	0.68

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

Publications

LitVar

Other links and lift over

dbSNP: rs76983681; hg19: chr19-42382757;