2-167385965-C-T

Variant names:

• chr2-167385965-C-T
• rs1523885
• NM_020981.4:c.-511+92631C>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.-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
• Publications: 0 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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.982 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020981.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	B3GALT1	NM_020981.4	MANE Select	c.-511+92631C>T		intron	N/A	NP_066191.1	Q9Y5Z6

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	B3GALT1	ENST00000392690.4	TSL:6 MANE Select	c.-511+92631C>T		intron	N/A	ENSP00000376456.2	Q9Y5Z6
	ENSG00000228222	ENST00000442316.1	TSL:3	n.164+92631C>T		intron	N/A

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

African (AFR) AF: 0.857 AC: 35572 AN: 41516

American (AMR) AF: 0.963 AC: 14725 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.946 AC: 3284 AN: 3472

East Asian (EAS) AF: 0.950 AC: 4916 AN: 5176

South Asian (SAS) AF: 0.928 AC: 4472 AN: 4820

European-Finnish (FIN) AF: 0.988 AC: 10496 AN: 10620

Middle Eastern (MID) AF: 0.949 AC: 279 AN: 294

European-Non Finnish (NFE) AF: 0.988 AC: 67242 AN: 68034

Other (OTH) AF: 0.945 AC: 1999 AN: 2116

Alfa AF: 0.963 Hom.: 9148

Bravo AF: 0.939

Asia WGS AF: 0.933 AC: 3245 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.4
DANN	Benign	0.49
PhyloP100		0.074

Splicing

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

Other links and lift over

dbSNP: rs1523885; hg19: chr2-168242475;