rs7921

Variant names:

• chr17-63928899-G-A
• rs7921
• NM_000626.4:c.*327C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 23 publications found

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]

CD79B Gene-Disease associations (from GenCC):

• agammaglobulinemia 6, autosomal recessive

  Inheritance: AR Classification: DEFINITIVE, STRONG, MODERATE Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae), ClinGen
• autosomal agammaglobulinemia

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

ENSG00000285947 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
CD79B	NM_000626.4	c.*327C>T		3_prime_UTR_variant	Exon 6 of 6	ENST00000006750.8	NP_000617.1
CD79B	NM_001039933.3	c.*327C>T		3_prime_UTR_variant	Exon 6 of 6		NP_001035022.1
CD79B	NM_001329050.2	c.*327C>T		3_prime_UTR_variant	Exon 5 of 5		NP_001315979.1
CD79B	NM_021602.4	c.*327C>T		3_prime_UTR_variant	Exon 5 of 5		NP_067613.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CD79B	ENST00000006750.8	c.*327C>T		3_prime_UTR_variant	Exon 6 of 6	1	NM_000626.4	ENSP00000006750.4
ENSG00000285947	ENST00000647774.1	c.286+350C>T		intron_variant	Intron 4 of 7			ENSP00000497443.1

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

African (AFR) AF: 0.269 AC: 2707 AN: 10072

American (AMR) AF: 0.151 AC: 2071 AN: 13674

Ashkenazi Jewish (ASJ) AF: 0.219 AC: 2287 AN: 10438

East Asian (EAS) AF: 0.0488 AC: 1015 AN: 20804

South Asian (SAS) AF: 0.185 AC: 7109 AN: 38398

European-Finnish (FIN) AF: 0.221 AC: 2839 AN: 12866

Middle Eastern (MID) AF: 0.242 AC: 319 AN: 1318

European-Non Finnish (NFE) AF: 0.255 AC: 44959 AN: 176636

Other (OTH) AF: 0.219 AC: 3940 AN: 17958

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

African (AFR) AF: 0.278 AC: 11494 AN: 41418

American (AMR) AF: 0.171 AC: 2613 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.219 AC: 760 AN: 3468

East Asian (EAS) AF: 0.0539 AC: 278 AN: 5160

South Asian (SAS) AF: 0.181 AC: 871 AN: 4812

European-Finnish (FIN) AF: 0.202 AC: 2136 AN: 10584

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.258 AC: 17536 AN: 67928

Other (OTH) AF: 0.219 AC: 463 AN: 2110

Alfa AF: 0.243 Hom.: 5448

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
PhyloP100		-0.029
Mutation Taster		=99/1	polymorphism (auto)

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

Other links and lift over

dbSNP: rs7921; hg19: chr17-62006259;