Variant chr17-49132804-C-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_001159387.2(B4GALNT2):c.12C>A(p.Gly4=) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00989 in 1,375,652 control chromosomes in the GnomAD database, including 103 homozygotes. In-silico tool predicts a benign outcome for this variant. 2/2 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0062 ( 6 hom., cov: 31)

Exomes 𝑓: 0.010 ( 97 hom. )

Consequence

B4GALNT2
NM_001159387.2 splice_region, synonymous

Scores

Splicing: ADA: 0.0001619

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.0340

Variant links:

Genes affected

B4GALNT2 (HGNC:24136): (beta-1,4-N-acetyl-galactosaminyltransferase 2 (SID blood group)) B4GALNT2 catalyzes the last step in the biosynthesis of the human Sd(a) antigen through the addition of an N-acetylgalactosamine residue via a beta-1,4 linkage to a subterminal galactose residue substituted with an alpha-2,3-linked sialic acid. B4GALNT2 also catalyzes the last step in the biosynthesis of the Cad antigen (Montiel et al., 2003 [PubMed 12678917]).[supplied by OMIM, Mar 2008]

B4GALNT2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.59).

BP6

Variant 17-49132804-C-A is Benign according to our data. Variant chr17-49132804-C-A is described in ClinVar as [Likely_benign]. Clinvar id is 2647886.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-0.034 with no splicing effect.

BS2

High Homozygotes in GnomAd4 at 6 BG gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
B4GALNT2	NM_001159387.2 linkuse as main transcript	c.12C>A	p.Gly4=	splice_region_variant, synonymous_variant	1/11	ENST00000393354.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
B4GALNT2	ENST00000393354.7 linkuse as main transcript	c.12C>A	p.Gly4=	splice_region_variant, synonymous_variant	1/11	1	NM_001159387.2	P1	Q8NHY0-2
B4GALNT2	ENST00000504681.5 linkuse as main transcript	c.-65+294C>A		intron_variant		2			Q8NHY0-3

Frequencies

GnomAD3 genomes

AF:

0.00620

AC:

943

AN:

152072

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00193

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00589

Gnomad ASJ

AF:

0.00836

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00684

Gnomad FIN

AF:

0.00132

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00993

Gnomad OTH

AF:

0.0105

GnomAD3 exomes

AF:

0.00541

AC:

154

AN:

28466

Hom.:

AF XY:

0.00530

AC XY:

AN XY:

13400

show subpopulations

Gnomad AFR exome

AF:

0.000636

Gnomad AMR exome

AF:

0.000700

Gnomad ASJ exome

AF:

0.00560

Gnomad EAS exome

AF:

0.00120

Gnomad SAS exome

AF:

0.00239

Gnomad FIN exome

AF:

0.00278

Gnomad NFE exome

AF:

0.00921

Gnomad OTH exome

AF:

0.00810

GnomAD4 exome

AF:

0.0104

AC:

12667

AN:

1223462

Hom.:

Cov.:

AF XY:

0.0100

AC XY:

5918

AN XY:

590832

show subpopulations

Gnomad4 AFR exome

AF:

0.00134

Gnomad4 AMR exome

AF:

0.00395

Gnomad4 ASJ exome

AF:

0.00952

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00406

Gnomad4 FIN exome

AF:

0.00257

Gnomad4 NFE exome

AF:

0.0116

Gnomad4 OTH exome

AF:

0.0104

GnomAD4 genome

AF:

0.00619

AC:

942

AN:

152190

Hom.:

Cov.:

AF XY:

0.00562

AC XY:

418

AN XY:

74406

show subpopulations

Gnomad4 AFR

AF:

0.00193

Gnomad4 AMR

AF:

0.00589

Gnomad4 ASJ

AF:

0.00836

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00664

Gnomad4 FIN

AF:

0.00132

Gnomad4 NFE

AF:

0.00993

Gnomad4 OTH

AF:

0.0104

Alfa

AF:

0.00484

Hom.:

Bravo

AF:

0.00606

Asia WGS

AF:

0.00144

AC:

AN:

3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

May 01, 2022

B4GALNT2: BP4, BP7, BS1 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.59

CADD

Benign

DANN

Benign

0.89

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.00016

dbscSNV1_RF

Benign

0.0080

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