17-63931077-C-T

Variant names:

• chr17-63931077-C-T
• rs2003549
• NM_000626.4:c.118+258G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 12 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 -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 VariationId 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

African (AFR) AF: 0.328 AC: 3746 AN: 11436

American (AMR) AF: 0.144 AC: 2957 AN: 20474

Ashkenazi Jewish (ASJ) AF: 0.217 AC: 2646 AN: 12202

East Asian (EAS) AF: 0.0471 AC: 1192 AN: 25282

South Asian (SAS) AF: 0.166 AC: 7834 AN: 47120

European-Finnish (FIN) AF: 0.221 AC: 4729 AN: 21392

Middle Eastern (MID) AF: 0.232 AC: 443 AN: 1912

European-Non Finnish (NFE) AF: 0.257 AC: 57485 AN: 223630

Other (OTH) AF: 0.216 AC: 4755 AN: 21964

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

African (AFR) AF: 0.328 AC: 13593 AN: 41456

American (AMR) AF: 0.177 AC: 2702 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.219 AC: 762 AN: 3472

East Asian (EAS) AF: 0.0542 AC: 280 AN: 5166

South Asian (SAS) AF: 0.154 AC: 743 AN: 4816

European-Finnish (FIN) AF: 0.201 AC: 2131 AN: 10602

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

European-Non Finnish (NFE) AF: 0.258 AC: 17540 AN: 67942

Other (OTH) AF: 0.232 AC: 489 AN: 2112

Alfa AF: 0.245 Hom.: 8249

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

Jun 18, 2021

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.8
DANN	Benign	0.64
PhyloP100		-0.84
PromoterAI		-0.027	Neutral
Mutation Taster		=100/0	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: rs2003549; hg19: chr17-62008437;