17-63929072-G-A

Position:

• chr17-63929072-G-A

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.*154C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.365 in 672,394 control chromosomes in the GnomAD database, including 47,280 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.32 (8693 hom., cov: 33)
  • Exomes 𝑓: 0.38 (38587 hom.)
• Consequence: CD79B NM_000626.4 3_prime_UTR
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 0.427

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=-0.78).
• BP6: Variant 17-63929072-G-A is Benign according to our data. Variant chr17-63929072-G-A is described in ClinVar as [Benign]. Clinvar id is 1231409.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.397 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CD79B	NM_000626.4	c.*154C>T		3_prime_UTR_variant	6/6	ENST00000006750.8	NP_000617.1
CD79B	NM_001039933.3	c.*154C>T		3_prime_UTR_variant	6/6		NP_001035022.1
CD79B	NM_001329050.2	c.*154C>T		3_prime_UTR_variant	5/5		NP_001315979.1
CD79B	NM_021602.4	c.*154C>T		3_prime_UTR_variant	5/5		NP_067613.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CD79B	ENST00000006750.8	c.*154C>T		3_prime_UTR_variant	6/6	1	NM_000626.4	ENSP00000006750	P4
CD79B	ENST00000392795.7	c.*154C>T		3_prime_UTR_variant	6/6	1		ENSP00000376544	A1
CD79B	ENST00000559358.1	n.855C>T		non_coding_transcript_exon_variant	4/4	2
CD79B	ENST00000698624.1	n.841C>T		non_coding_transcript_exon_variant	5/5

Frequencies

GnomAD3 genomes AF: 0.318 AC: 48278 AN: 151930 Hom.: 8686 Cov.: 33

Gnomad AFR AF: 0.137

Gnomad AMI AF: 0.471

Gnomad AMR AF: 0.334

Gnomad ASJ AF: 0.428

Gnomad EAS AF: 0.404

Gnomad SAS AF: 0.278

Gnomad FIN AF: 0.381

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.401

Gnomad OTH AF: 0.353

GnomAD4 exome AF: 0.379 AC: 197285 AN: 520346 Hom.: 38587 Cov.: 4 AF XY: 0.376 AC XY: 104881 AN XY: 278988

Gnomad4 AFR exome AF: 0.136

Gnomad4 AMR exome AF: 0.350

Gnomad4 ASJ exome AF: 0.441

Gnomad4 EAS exome AF: 0.415

Gnomad4 SAS exome AF: 0.294

Gnomad4 FIN exome AF: 0.370

Gnomad4 NFE exome AF: 0.403

Gnomad4 OTH exome AF: 0.386

GnomAD4 genome AF: 0.318 AC: 48310 AN: 152048 Hom.: 8693 Cov.: 33 AF XY: 0.316 AC XY: 23456 AN XY: 74298

Gnomad4 AFR AF: 0.137

Gnomad4 AMR AF: 0.334

Gnomad4 ASJ AF: 0.428

Gnomad4 EAS AF: 0.403

Gnomad4 SAS AF: 0.279

Gnomad4 FIN AF: 0.381

Gnomad4 NFE AF: 0.401

Gnomad4 OTH AF: 0.356

Alfa AF: 0.366 Hom.: 3321

Bravo AF: 0.311

Asia WGS AF: 0.334 AC: 1165 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
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	-0.78
CADD	Benign	14
DANN	Benign	0.59

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.11		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: rs12603821; hg19: chr17-62006432;