17-63929137-A-G

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_000626.4(CD79B):c.*89T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.62 in 897,194 control chromosomes in the GnomAD database, including 175,341 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.63 (30737 hom., cov: 33)
  • Exomes 𝑓: 0.62 (144604 hom.)
• Consequence: CD79B NM_000626.4 3_prime_UTR
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.285

Genes affected

CD79B (HGNC:1699): (CD79b 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-beta 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 -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BP6: Variant 17-63929137-A-G is Benign according to our data. Variant chr17-63929137-A-G is described in ClinVar as [Benign]. Clinvar id is 1287682.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.666 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CD79B	NM_000626.4	c.*89T>C		3_prime_UTR_variant	6/6	ENST00000006750.8
CD79B	NM_001039933.3	c.*89T>C		3_prime_UTR_variant	6/6
CD79B	NM_001329050.2	c.*89T>C		3_prime_UTR_variant	5/5
CD79B	NM_021602.4	c.*89T>C		3_prime_UTR_variant	5/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CD79B	ENST00000006750.8	c.*89T>C		3_prime_UTR_variant	6/6	1	NM_000626.4	P4
CD79B	ENST00000392795.7	c.*89T>C		3_prime_UTR_variant	6/6	1		A1
CD79B	ENST00000559358.1	n.790T>C		non_coding_transcript_exon_variant	4/4	2
CD79B	ENST00000698624.1	n.776T>C		non_coding_transcript_exon_variant	5/5

Frequencies

GnomAD3 genomes AF: 0.633 AC: 96113 AN: 151876 Hom.: 30721 Cov.: 33

Gnomad AFR AF: 0.673

Gnomad AMI AF: 0.765

Gnomad AMR AF: 0.532

Gnomad ASJ AF: 0.664

Gnomad EAS AF: 0.464

Gnomad SAS AF: 0.440

Gnomad FIN AF: 0.585

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.662

Gnomad OTH AF: 0.631

GnomAD4 exome AF: 0.617 AC: 460053 AN: 745200 Hom.: 144604 Cov.: 10 AF XY: 0.612 AC XY: 242657 AN XY: 396176

Gnomad4 AFR exome AF: 0.670

Gnomad4 AMR exome AF: 0.499

Gnomad4 ASJ exome AF: 0.674

Gnomad4 EAS exome AF: 0.463

Gnomad4 SAS exome AF: 0.461

Gnomad4 FIN exome AF: 0.589

Gnomad4 NFE exome AF: 0.661

Gnomad4 OTH exome AF: 0.624

GnomAD4 genome AF: 0.633 AC: 96169 AN: 151994 Hom.: 30737 Cov.: 33 AF XY: 0.622 AC XY: 46235 AN XY: 74276

Gnomad4 AFR AF: 0.672

Gnomad4 AMR AF: 0.531

Gnomad4 ASJ AF: 0.664

Gnomad4 EAS AF: 0.463

Gnomad4 SAS AF: 0.440

Gnomad4 FIN AF: 0.585

Gnomad4 NFE AF: 0.662

Gnomad4 OTH AF: 0.631

Alfa AF: 0.645 Hom.: 27893

Bravo AF: 0.632

Asia WGS AF: 0.462 AC: 1609 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not specified Benign:1

Benign, criteria provided, single submitter

clinical testing

Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan

Jan 24, 2024

This variant is classified as Benign based on local population frequency. This variant was detected in 36% of patients studied by a panel of primary immunodeficiencies. Number of patients: 34. Only high quality variants are reported. -

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 10, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	2.1
Dann	Benign	0.61

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

Publications

LitVar

Other links and lift over

dbSNP: rs1051684; hg19: chr17-62006497; COSMIC: COSV50079704; COSMIC: COSV50079704;