2-167483916-C-T

Position:

• chr2-167483916-C-T

Variant summary

Our verdict is Benign. Variant got -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

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
B3GALT1	NM_020981.4	c.-510-6261C>T		intron_variant		ENST00000392690.4	NP_066191.1
B3GALT1	XM_047446159.1	c.-6771C>T		5_prime_UTR_variant	1/4		XP_047302115.1
B3GALT1	XM_011512085.3	c.-526-6261C>T		intron_variant			XP_011510387.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
B3GALT1	ENST00000392690.4	c.-510-6261C>T		intron_variant			NM_020981.4	ENSP00000376456	P1
	ENST00000442316.1	n.165-6261C>T		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.436

Gnomad4 AMR AF: 0.381

Gnomad4 ASJ AF: 0.424

Gnomad4 EAS AF: 0.838

Gnomad4 SAS AF: 0.570

Gnomad4 FIN AF: 0.256

Gnomad4 NFE AF: 0.339

Gnomad4 OTH AF: 0.434

Alfa AF: 0.360 Hom.: 17157

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1919854; hg19: chr2-168340426;