Variant rs6512586 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_004776.4(B4GALT5):c.116-27907C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.526 in 517,860 control chromosomes in the GnomAD database, including 73,488 homozygotes. 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: 𝑓 0.49 ( 18689 hom., cov: 32)

Exomes 𝑓: 0.54 ( 54799 hom. )

Consequence

B4GALT5
NM_004776.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.989

Variant links:

Genes affected

B4GALT5 (HGNC:928): (beta-1,4-galactosyltransferase 5) This gene is one of seven beta-1,4-galactosyltransferase (beta4GalT) genes. They encode type II membrane-bound glycoproteins that appear to have exclusive specificity for the donor substrate UDP-galactose; all transfer galactose in a beta1,4 linkage to similar acceptor sugars: GlcNAc, Glc, and Xyl. Each beta4GalT has a distinct function in the biosynthesis of different glycoconjugates and saccharide structures. As type II membrane proteins, they have an N-terminal hydrophobic signal sequence that directs the protein to the Golgi apparatus and which then remains uncleaved to function as a transmembrane anchor. By sequence similarity, the beta4GalTs form four groups: beta4GalT1 and beta4GalT2, beta4GalT3 and beta4GalT4, beta4GalT5 and beta4GalT6, and beta4GalT7. The function of the enzyme encoded by this gene is not clear. This gene was previously designated as B4GALT4 but was renamed to B4GALT5. In the literature it is also referred to as beta4GalT2. [provided by RefSeq, Jul 2008]

B4GALT5 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.97).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.633 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
B4GALT5	NM_004776.4 linkuse as main transcript	c.116-27907C>T		intron_variant		ENST00000371711.4	NP_004767.1	O43286

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
B4GALT5	ENST00000371711.4 linkuse as main transcript	c.116-27907C>T		intron_variant		1	NM_004776.4	ENSP00000360776.4		O43286

Frequencies

GnomAD3 genomes

AF:

0.490

AC:

74350

AN:

151690

Hom.:

18677

Cov.:

show subpopulations

Gnomad AFR

AF:

0.388

Gnomad AMI

AF:

0.549

Gnomad AMR

AF:

0.466

Gnomad ASJ

AF:

0.534

Gnomad EAS

AF:

0.388

Gnomad SAS

AF:

0.650

Gnomad FIN

AF:

0.503

Gnomad MID

AF:

0.602

Gnomad NFE

AF:

0.549

Gnomad OTH

AF:

0.497

GnomAD3 exomes

AF:

0.518

AC:

118033

AN:

227938

Hom.:

31489

AF XY:

0.533

AC XY:

67288

AN XY:

126140

show subpopulations

Gnomad AFR exome

AF:

0.375

Gnomad AMR exome

AF:

0.448

Gnomad ASJ exome

AF:

0.522

Gnomad EAS exome

AF:

0.370

Gnomad SAS exome

AF:

0.652

Gnomad FIN exome

AF:

0.504

Gnomad NFE exome

AF:

0.546

Gnomad OTH exome

AF:

0.529

GnomAD4 exome

AF:

0.541

AC:

198006

AN:

366052

Hom.:

54799

Cov.:

AF XY:

0.555

AC XY:

116397

AN XY:

209876

show subpopulations

Gnomad4 AFR exome

AF:

0.375

Gnomad4 AMR exome

AF:

0.450

Gnomad4 ASJ exome

AF:

0.524

Gnomad4 EAS exome

AF:

0.377

Gnomad4 SAS exome

AF:

0.652

Gnomad4 FIN exome

AF:

0.506

Gnomad4 NFE exome

AF:

0.543

Gnomad4 OTH exome

AF:

0.541

GnomAD4 genome

AF:

0.490

AC:

74395

AN:

151808

Hom.:

18689

Cov.:

AF XY:

0.490

AC XY:

36346

AN XY:

74192

show subpopulations

Gnomad4 AFR

AF:

0.387

Gnomad4 AMR

AF:

0.467

Gnomad4 ASJ

AF:

0.534

Gnomad4 EAS

AF:

0.388

Gnomad4 SAS

AF:

0.652

Gnomad4 FIN

AF:

0.503

Gnomad4 NFE

AF:

0.549

Gnomad4 OTH

AF:

0.499

Alfa

AF:

0.537

Hom.:

36365

Bravo

AF:

0.481

Asia WGS

AF:

0.570

AC:

1981

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

0.49

DANN

Benign

0.67

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over