17-63931077-C-T

Variant names:

• chr17-63931077-C-T
• rs2003549
• NM_000626.4:c.118+258G>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.118+258G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.231 in 537,484 control chromosomes in the GnomAD database, including 15,780 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.25 (5168 hom., cov: 32)
  • Exomes 𝑓: 0.22 (10612 hom.)
• Consequence: CD79B NM_000626.4 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.841

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]

ENSG00000285947 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BP6: Variant 17-63931077-C-T is Benign according to our data. Variant chr17-63931077-C-T is described in ClinVar as [Benign]. Clinvar id is 1291751.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.323 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CD79B	NM_000626.4	c.118+258G>A		intron_variant	Intron 2 of 5	ENST00000006750.8	NP_000617.1
CD79B	NM_001039933.3	c.121+258G>A		intron_variant	Intron 2 of 5		NP_001035022.1
CD79B	NM_001329050.2	c.121+258G>A		intron_variant	Intron 2 of 4		NP_001315979.1
CD79B	NM_021602.4	c.118+258G>A		intron_variant	Intron 2 of 4		NP_067613.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CD79B	ENST00000006750.8	c.118+258G>A		intron_variant	Intron 2 of 5	1	NM_000626.4	ENSP00000006750.4
ENSG00000285947	ENST00000647774.1	c.49+258G>A		intron_variant	Intron 1 of 7			ENSP00000497443.1

Frequencies

GnomAD3 genomes AF: 0.254 AC: 38587 AN: 151954 Hom.: 5174 Cov.: 32

Gnomad AFR AF: 0.328

Gnomad AMI AF: 0.293

Gnomad AMR AF: 0.177

Gnomad ASJ AF: 0.219

Gnomad EAS AF: 0.0543

Gnomad SAS AF: 0.156

Gnomad FIN AF: 0.201

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.258

Gnomad OTH AF: 0.234

GnomAD4 exome AF: 0.223 AC: 85787 AN: 385412 Hom.: 10612 Cov.: 2 AF XY: 0.219 AC XY: 44806 AN XY: 204262

Gnomad4 AFR exome AF: 0.328

Gnomad4 AMR exome AF: 0.144

Gnomad4 ASJ exome AF: 0.217

Gnomad4 EAS exome AF: 0.0471

Gnomad4 SAS exome AF: 0.166

Gnomad4 FIN exome AF: 0.221

Gnomad4 NFE exome AF: 0.257

Gnomad4 OTH exome AF: 0.216

GnomAD4 genome AF: 0.254 AC: 38590 AN: 152072 Hom.: 5168 Cov.: 32 AF XY: 0.247 AC XY: 18355 AN XY: 74352

Gnomad4 AFR AF: 0.328

Gnomad4 AMR AF: 0.177

Gnomad4 ASJ AF: 0.219

Gnomad4 EAS AF: 0.0542

Gnomad4 SAS AF: 0.154

Gnomad4 FIN AF: 0.201

Gnomad4 NFE AF: 0.258

Gnomad4 OTH AF: 0.232

Alfa AF: 0.245 Hom.: 5917

Bravo AF: 0.253

Asia WGS AF: 0.0990 AC: 347 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

-

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Jun 18, 2021

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.8
DANN	Benign	0.64

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: rs2003549; hg19: chr17-62008437;