2-167785460-A-G

Variant names:

• chr2-167785460-A-G
• rs1004368
• NM_020981.4:c.-351-33212A>G

Variant summary

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

The NM_020981.4(B3GALT1):​c.-351-33212A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.283 in 152,070 control chromosomes in the GnomAD database, including 7,449 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 0.28 (7449 hom., cov: 32)
• Consequence: B3GALT1 NM_020981.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.109
• Publications: 4 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]

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 (AFR) allele frequency at 95% confidence interval = 0.478 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	B3GALT1	NM_020981.4	MANE Select	c.-351-33212A>G		intron	N/A	NP_066191.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	B3GALT1	ENST00000392690.4	TSL:6 MANE Select	c.-351-33212A>G		intron	N/A	ENSP00000376456.2
	B3GALT1	ENST00000970731.1		c.-351-33212A>G		intron	N/A	ENSP00000640790.1

Frequencies

GnomAD3 genomes AF: 0.283 AC: 42998 AN: 151950 Hom.: 7437 Cov.: 32

Gnomad AFR AF: 0.484

Gnomad AMI AF: 0.302

Gnomad AMR AF: 0.179

Gnomad ASJ AF: 0.269

Gnomad EAS AF: 0.332

Gnomad SAS AF: 0.286

Gnomad FIN AF: 0.189

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.196

Gnomad OTH AF: 0.269

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

GnomAD4 genome AF: 0.283 AC: 43040 AN: 152070 Hom.: 7449 Cov.: 32 AF XY: 0.281 AC XY: 20872 AN XY: 74350

African (AFR) AF: 0.483 AC: 20039 AN: 41446

American (AMR) AF: 0.179 AC: 2728 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.269 AC: 934 AN: 3472

East Asian (EAS) AF: 0.332 AC: 1719 AN: 5170

South Asian (SAS) AF: 0.288 AC: 1384 AN: 4810

European-Finnish (FIN) AF: 0.189 AC: 2001 AN: 10592

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.196 AC: 13322 AN: 67990

Other (OTH) AF: 0.270 AC: 571 AN: 2112

Alfa AF: 0.246 Hom.: 9122

Bravo AF: 0.289

Asia WGS AF: 0.329 AC: 1146 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.7
DANN	Benign	0.32
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs1004368; hg19: chr2-168641970;