dbSNP rs1919854: B3GALT1:c.-510-6261C>T (chr2-167483916-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_020981.4(B3GALT1):c.-510-6261C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.392 in 151,860 control chromosomes in the GnomAD database, including 12,548 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 0.39 ( 12548 hom., cov: 32)

Consequence

B3GALT1
NM_020981.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.233

Publications

2 publications found

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 was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-1.0).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.817 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
B3GALT1	NM_020981.4 link	c.-510-6261C>T	intron_variant	Intron 1 of 4	ENST00000392690.4	NP_066191.1	Q9Y5Z6
B3GALT1	XM_047446159.1 link	c.-6771C>T	5_prime_UTR_variant	Exon 1 of 4		XP_047302115.1
B3GALT1	XM_011512085.3 link	c.-526-6261C>T	intron_variant	Intron 1 of 4		XP_011510387.1	Q9Y5Z6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
B3GALT1	ENST00000392690.4 link	c.-510-6261C>T		intron_variant	Intron 1 of 4	6	NM_020981.4	ENSP00000376456.2		Q9Y5Z6
ENSG00000228222	ENST00000442316.1 link	n.165-6261C>T		intron_variant	Intron 1 of 2	3

Frequencies

GnomAD3 genomes

AF:

0.392

AC:

59444

AN:

151740

Hom.:

12535

Cov.:

show subpopulations

Gnomad AFR

AF:

0.436

Gnomad AMI

AF:

0.305

Gnomad AMR

AF:

0.381

Gnomad ASJ

AF:

0.424

Gnomad EAS

AF:

0.838

Gnomad SAS

AF:

0.571

Gnomad FIN

AF:

0.256

Gnomad MID

AF:

0.509

Gnomad NFE

AF:

0.339

Gnomad OTH

AF:

0.429

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

GnomAD4 genome

AF:

0.392

AC:

59501

AN:

151860

Hom.:

12548

Cov.:

AF XY:

0.394

AC XY:

29263

AN XY:

74242

show subpopulations

African (AFR)

AF:

0.436

AC:

18043

AN:

41340

American (AMR)

AF:

0.381

AC:

5818

AN:

15262

Ashkenazi Jewish (ASJ)

AF:

0.424

AC:

1470

AN:

3464

East Asian (EAS)

AF:

0.838

AC:

4328

AN:

5166

South Asian (SAS)

AF:

0.570

AC:

2744

AN:

4816

European-Finnish (FIN)

AF:

0.256

AC:

2703

AN:

10554

Middle Eastern (MID)

AF:

0.510

AC:

150

AN:

294

European-Non Finnish (NFE)

AF:

0.339

AC:

23053

AN:

67946

Other (OTH)

AF:

0.434

AC:

914

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1768

3537

5305

7074

8842

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

586

1172

1758

2344

2930

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.364

Hom.:

39942

Bravo

AF:

0.401

Asia WGS

AF:

0.671

AC:

2328

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

1.1

(source)

DANN

Benign

0.50

PhyloP100

-0.23

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over