Variant 17-63929137-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_000626.4(CD79B):c.*89T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.62 in 897,194 control chromosomes in the GnomAD database, including 175,341 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.63 ( 30737 hom., cov: 33)

Exomes 𝑓: 0.62 ( 144604 hom. )

Consequence

CD79B
NM_000626.4 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -0.285

Variant links:

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 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BP6

Variant 17-63929137-A-G is Benign according to our data. Variant chr17-63929137-A-G is described in ClinVar as [Benign]. Clinvar id is 1287682.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.666 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	MANE	Protein
CD79B	NM_000626.4 linkuse as main transcript	c.*89T>C	3_prime_UTR_variant	6/6	ENST00000006750.8	NP_000617.1
CD79B	NM_001039933.3 linkuse as main transcript	c.*89T>C	3_prime_UTR_variant	6/6		NP_001035022.1
CD79B	NM_001329050.2 linkuse as main transcript	c.*89T>C	3_prime_UTR_variant	5/5		NP_001315979.1
CD79B	NM_021602.4 linkuse as main transcript	c.*89T>C	3_prime_UTR_variant	5/5		NP_067613.1

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CD79B	ENST00000006750.8 linkuse as main transcript	c.*89T>C	3_prime_UTR_variant	6/6	1	NM_000626.4	ENSP00000006750	P4	P40259-1
CD79B	ENST00000392795.7 linkuse as main transcript	c.*89T>C	3_prime_UTR_variant	6/6	1		ENSP00000376544	A1	P40259-3
CD79B	ENST00000559358.1 linkuse as main transcript	n.790T>C	non_coding_transcript_exon_variant	4/4	2
CD79B	ENST00000698624.1 linkuse as main transcript	n.776T>C	non_coding_transcript_exon_variant	5/5

Frequencies

GnomAD3 genomes

AF:

0.633

AC:

96113

AN:

151876

Hom.:

30721

Cov.:

show subpopulations

Gnomad AFR

AF:

0.673

Gnomad AMI

AF:

0.765

Gnomad AMR

AF:

0.532

Gnomad ASJ

AF:

0.664

Gnomad EAS

AF:

0.464

Gnomad SAS

AF:

0.440

Gnomad FIN

AF:

0.585

Gnomad MID

AF:

0.734

Gnomad NFE

AF:

0.662

Gnomad OTH

AF:

0.631

GnomAD4 exome

AF:

0.617

AC:

460053

AN:

745200

Hom.:

144604

Cov.:

AF XY:

0.612

AC XY:

242657

AN XY:

396176

show subpopulations

Gnomad4 AFR exome

AF:

0.670

Gnomad4 AMR exome

AF:

0.499

Gnomad4 ASJ exome

AF:

0.674

Gnomad4 EAS exome

AF:

0.463

Gnomad4 SAS exome

AF:

0.461

Gnomad4 FIN exome

AF:

0.589

Gnomad4 NFE exome

AF:

0.661

Gnomad4 OTH exome

AF:

0.624

GnomAD4 genome

AF:

0.633

AC:

96169

AN:

151994

Hom.:

30737

Cov.:

AF XY:

0.622

AC XY:

46235

AN XY:

74276

show subpopulations

Gnomad4 AFR

AF:

0.672

Gnomad4 AMR

AF:

0.531

Gnomad4 ASJ

AF:

0.664

Gnomad4 EAS

AF:

0.463

Gnomad4 SAS

AF:

0.440

Gnomad4 FIN

AF:

0.585

Gnomad4 NFE

AF:

0.662

Gnomad4 OTH

AF:

0.631

Alfa

AF:

0.645

Hom.:

27893

Bravo

AF:

0.632

Asia WGS

AF:

0.462

AC:

1609

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Nov 10, 2018	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan

Jan 24, 2024

This variant is classified as Benign based on local population frequency. This variant was detected in 36% of patients studied by a panel of primary immunodeficiencies. Number of patients: 34. Only high quality variants are reported. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

2.1

DANN

Benign

0.61

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over