rs10497325

Variant names:

• chr2-167518242-A-C
• rs10497325
• NM_020981.4:c.-410+27965A>C

Your query was ambiguous. Multiple possible variants found:

• chr2-167518242-A-C
• chr2-167518242-A-G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000392690.4(B3GALT1):​c.-410+27965A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.022 in 152,242 control chromosomes in the GnomAD database, including 51 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 0.022 (51 hom., cov: 32)
• Consequence: B3GALT1 ENST00000392690.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.260
• 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=-0.92).
• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.022 (3347/152242) while in subpopulation AFR AF = 0.0389 (1615/41554). AF 95% confidence interval is 0.0373. There are 51 homozygotes in GnomAd4. There are 1667 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 51 AR gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000392690.4. 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.-410+27965A>C		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.-410+27965A>C		intron	N/A	ENSP00000376456.2
	ENSG00000228222	ENST00000442316.1	TSL:3	n.265+27965A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0220 AC: 3342 AN: 152124 Hom.: 50 Cov.: 32

Gnomad AFR AF: 0.0388

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0163

Gnomad ASJ AF: 0.0265

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.0108

Gnomad FIN AF: 0.0285

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0145

Gnomad OTH AF: 0.0201

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

GnomAD4 genome AF: 0.0220 AC: 3347 AN: 152242 Hom.: 51 Cov.: 32 AF XY: 0.0224 AC XY: 1667 AN XY: 74446

African (AFR) AF: 0.0389 AC: 1615 AN: 41554

American (AMR) AF: 0.0163 AC: 249 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0265 AC: 92 AN: 3472

East Asian (EAS) AF: 0.000579 AC: 3 AN: 5180

South Asian (SAS) AF: 0.0110 AC: 53 AN: 4820

European-Finnish (FIN) AF: 0.0285 AC: 303 AN: 10614

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0144 AC: 982 AN: 68002

Other (OTH) AF: 0.0199 AC: 42 AN: 2112

Alfa AF: 0.0212 Hom.: 13

Bravo AF: 0.0222

Asia WGS AF: 0.0100 AC: 37 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	6.3
DANN	Benign	0.68
PhyloP100		0.26
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs10497325; hg19: chr2-168374752;