dbSNP rs10497325: B3GALT1:c.-410+27965A>C (chr2-167518242-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2

The NM_020981.4(B3GALT1):c.-410+27965A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.022 in 152,242 control chromosomes in the GnomAD database, including 51 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 0.022 ( 51 hom., cov: 32)

Consequence

B3GALT1
NM_020981.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.260

Variant links:

Genes affected

B3GALT1 (HGNC:916): (beta-1,3-galactosyltransferase 1) This gene is a member of the beta-1,3-galactosyltransferase (beta3GalT) gene family. This family encodes type II membrane-bound glycoproteins with diverse enzymatic functions using different donor substrates (UDP-galactose and UDP-N-acetylglucosamine) and different acceptor sugars (N-acetylglucosamine, galactose, N-acetylgalactosamine). The beta3GalT genes are distantly related to the Drosophila Brainiac gene and have the protein coding sequence contained in a single exon. The beta3GalT proteins also contain conserved sequences not found in the beta4GalT or alpha3GalT proteins. The carbohydrate chains synthesized by these enzymes are designated as type 1, whereas beta4GalT enzymes synthesize type 2 carbohydrate chains. The ratio of type 1:type 2 chains changes during embryogenesis. By sequence similarity, the beta3GalT genes fall into at least two groups: beta3GalT4 and 4 other beta3GalT genes (beta3GalT1-3, beta3GalT5). This gene is expressed exclusively in the brain. The encoded protein shows strict donor substrate specificity for UDP-galactose. [provided by RefSeq, Jul 2008]

B3GALT1 links:

ENSG00000228222 (HGNC:):

ENSG00000228222 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=-0.92).

BS1

Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.022 (3347/152242) while in subpopulation AFR AF= 0.0389 (1615/41554). AF 95% confidence interval is 0.0373. There are 51 homozygotes in gnomad4. There are 1667 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 51 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
B3GALT1	NM_020981.4 link	c.-410+27965A>C	intron_variant	Intron 2 of 4	ENST00000392690.4	NP_066191.1	Q9Y5Z6
B3GALT1	XM_011512085.3 link	c.-426+27965A>C	intron_variant	Intron 2 of 4		XP_011510387.1	Q9Y5Z6
B3GALT1	XM_047446159.1 link	c.-410+27965A>C	intron_variant	Intron 1 of 3		XP_047302115.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
B3GALT1	ENST00000392690.4 link	c.-410+27965A>C		intron_variant	Intron 2 of 4	6	NM_020981.4	ENSP00000376456.2		Q9Y5Z6
ENSG00000228222	ENST00000442316.1 link	n.265+27965A>C		intron_variant	Intron 2 of 2	3

Frequencies

GnomAD3 genomes

AF:

0.0220

AC:

3342

AN:

152124

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0388

Gnomad AMI

AF:

0.00110

Gnomad AMR

AF:

0.0163

Gnomad ASJ

AF:

0.0265

Gnomad EAS

AF:

0.000578

Gnomad SAS

AF:

0.0108

Gnomad FIN

AF:

0.0285

Gnomad MID

AF:

0.0253

Gnomad NFE

AF:

0.0145

Gnomad OTH

AF:

0.0201

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.0220

AC:

3347

AN:

152242

Hom.:

Cov.:

AF XY:

0.0224

AC XY:

1667

AN XY:

74446

show subpopulations

Gnomad4 AFR

AF:

0.0389

Gnomad4 AMR

AF:

0.0163

Gnomad4 ASJ

AF:

0.0265

Gnomad4 EAS

AF:

0.000579

Gnomad4 SAS

AF:

0.0110

Gnomad4 FIN

AF:

0.0285

Gnomad4 NFE

AF:

0.0144

Gnomad4 OTH

AF:

0.0199

Alfa

AF:

0.00870

Hom.:

Bravo

AF:

0.0222

Asia WGS

AF:

0.0100

AC:

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

6.3

DANN

Benign

0.68

Splicing

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