NM_020981.4:c.-510-6261C>T

Variant names:

• chr2-167483916-C-T
• rs1919854
• NM_020981.4:c.-510-6261C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.233
• Publications: 2 publications found

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]

ENSG00000228222 (HGNC:):

ACMG classification

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.392 AC: 59444 AN: 151740 Hom.: 12535 Cov.: 32

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.: 32 AF XY: 0.394 AC XY: 29263 AN XY: 74242

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

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
DANN	Benign	0.50
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs1919854; hg19: chr2-168340426;