rs10497325

chr2-167518242-A-Cchr2-167518242-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NM_020981.4(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 NM_020981.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.260

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=-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 male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 50 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
B3GALT1	NM_020981.4	c.-410+27965A>C		intron_variant		ENST00000392690.4
B3GALT1	XM_011512085.3	c.-426+27965A>C		intron_variant
B3GALT1	XM_047446159.1	c.-410+27965A>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
B3GALT1	ENST00000392690.4	c.-410+27965A>C		intron_variant			NM_020981.4	P1
	ENST00000442316.1	n.265+27965A>C		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.0389

Gnomad4 AMR AF: 0.0163

Gnomad4 ASJ AF: 0.0265

Gnomad4 EAS AF: 0.000579

Gnomad4 SAS AF: 0.0110

Gnomad4 FIN AF: 0.0285

Gnomad4 NFE AF: 0.0144

Gnomad4 OTH AF: 0.0199

Alfa AF: 0.00870 Hom.: 3

Bravo AF: 0.0222

Asia WGS AF: 0.0100 AC: 37 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	6.3
Dann	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10497325; hg19: chr2-168374752;