NM_000626.4:c.118+258G>T

Variant names:

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

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_000626.4(CD79B):​c.118+258G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: CD79B NM_000626.4 intron
• Clinical Significance: Not reported in ClinVar
• 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CD79B	NM_000626.4	c.118+258G>T		intron_variant	Intron 2 of 5	ENST00000006750.8	NP_000617.1
CD79B	NM_001039933.3	c.121+258G>T		intron_variant	Intron 2 of 5		NP_001035022.1
CD79B	NM_001329050.2	c.121+258G>T		intron_variant	Intron 2 of 4		NP_001315979.1
CD79B	NM_021602.4	c.118+258G>T		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>T		intron_variant	Intron 2 of 5	1	NM_000626.4	ENSP00000006750.4
ENSG00000285947	ENST00000647774.1	c.49+258G>T		intron_variant	Intron 1 of 7			ENSP00000497443.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 385938 Hom.: 0 Cov.: 2 AF XY: 0.00 AC XY: 0 AN XY: 204552

African (AFR) AF: 0.00 AC: 0 AN: 11448

American (AMR) AF: 0.00 AC: 0 AN: 20480

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 12222

East Asian (EAS) AF: 0.00 AC: 0 AN: 25294

South Asian (SAS) AF: 0.00 AC: 0 AN: 47136

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 21448

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1914

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 224002

Other (OTH) AF: 0.00 AC: 0 AN: 21994

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 8249

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.4
DANN	Benign	0.53
PhyloP100		-0.84
PromoterAI		-0.011	Neutral

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;