2-167385965-C-T

Position:

• chr2-167385965-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.-511+92631C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.945 in 152,256 control chromosomes in the GnomAD database, including 68,238 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 0.95 (68238 hom., cov: 32)
• Consequence: B3GALT1 NM_020981.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0740

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.982 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
B3GALT1	NM_020981.4	c.-511+92631C>T		intron_variant		ENST00000392690.4	NP_066191.1
B3GALT1	XM_011512085.3	c.-527+92631C>T		intron_variant			XP_011510387.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
B3GALT1	ENST00000392690.4	c.-511+92631C>T		intron_variant		6	NM_020981.4	ENSP00000376456.2
ENSG00000228222	ENST00000442316.1	n.164+92631C>T		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.945 AC: 143798 AN: 152138 Hom.: 68196 Cov.: 32

Gnomad AFR AF: 0.857

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.963

Gnomad ASJ AF: 0.946

Gnomad EAS AF: 0.950

Gnomad SAS AF: 0.928

Gnomad FIN AF: 0.988

Gnomad MID AF: 0.949

Gnomad NFE AF: 0.988

Gnomad OTH AF: 0.944

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

GnomAD4 genome AF: 0.945 AC: 143897 AN: 152256 Hom.: 68238 Cov.: 32 AF XY: 0.945 AC XY: 70390 AN XY: 74462

Gnomad4 AFR AF: 0.857

Gnomad4 AMR AF: 0.963

Gnomad4 ASJ AF: 0.946

Gnomad4 EAS AF: 0.950

Gnomad4 SAS AF: 0.928

Gnomad4 FIN AF: 0.988

Gnomad4 NFE AF: 0.988

Gnomad4 OTH AF: 0.945

Alfa AF: 0.968 Hom.: 8864

Bravo AF: 0.939

Asia WGS AF: 0.933 AC: 3245 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.4
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1523885; hg19: chr2-168242475;