rs7921

Positions:

• chr17-63928899-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000626.4(CD79B):​c.*327C>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 0.228 in 454,144 control chromosomes in the GnomAD database, including 12,715 homozygotes. 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: 𝑓 0.24 (4561 hom., cov: 32)
  • Exomes 𝑓: 0.22 (8154 hom.)
• Consequence: CD79B NM_000626.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0290

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.273 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CD79B	NM_000626.4	c.*327C>T		3_prime_UTR_variant	6/6	ENST00000006750.8
CD79B	NM_001039933.3	c.*327C>T		3_prime_UTR_variant	6/6
CD79B	NM_001329050.2	c.*327C>T		3_prime_UTR_variant	5/5
CD79B	NM_021602.4	c.*327C>T		3_prime_UTR_variant	5/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CD79B	ENST00000006750.8	c.*327C>T		3_prime_UTR_variant	6/6	1	NM_000626.4	P4
CD79B	ENST00000392795.7	c.*327C>T		3_prime_UTR_variant	6/6	1		A1
CD79B	ENST00000559358.1	n.1028C>T		non_coding_transcript_exon_variant	4/4	2
CD79B	ENST00000698624.1	n.1014C>T		non_coding_transcript_exon_variant	5/5

Frequencies

GnomAD3 genomes AF: 0.240 AC: 36502 AN: 151862 Hom.: 4567 Cov.: 32

Gnomad AFR AF: 0.278

Gnomad AMI AF: 0.293

Gnomad AMR AF: 0.171

Gnomad ASJ AF: 0.219

Gnomad EAS AF: 0.0539

Gnomad SAS AF: 0.183

Gnomad FIN AF: 0.202

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.258

Gnomad OTH AF: 0.222

GnomAD4 exome AF: 0.223 AC: 67246 AN: 302164 Hom.: 8154 Cov.: 0 AF XY: 0.220 AC XY: 34333 AN XY: 156110

Gnomad4 AFR exome AF: 0.269

Gnomad4 AMR exome AF: 0.151

Gnomad4 ASJ exome AF: 0.219

Gnomad4 EAS exome AF: 0.0488

Gnomad4 SAS exome AF: 0.185

Gnomad4 FIN exome AF: 0.221

Gnomad4 NFE exome AF: 0.255

Gnomad4 OTH exome AF: 0.219

GnomAD4 genome AF: 0.240 AC: 36501 AN: 151980 Hom.: 4561 Cov.: 32 AF XY: 0.234 AC XY: 17421 AN XY: 74298

Gnomad4 AFR AF: 0.278

Gnomad4 AMR AF: 0.171

Gnomad4 ASJ AF: 0.219

Gnomad4 EAS AF: 0.0539

Gnomad4 SAS AF: 0.181

Gnomad4 FIN AF: 0.202

Gnomad4 NFE AF: 0.258

Gnomad4 OTH AF: 0.219

Alfa AF: 0.243 Hom.: 4448

Bravo AF: 0.236

Asia WGS AF: 0.109 AC: 382 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.8
DANN	Benign	0.43

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: rs7921; hg19: chr17-62006259;