rs10497327

chr2-167660305-G-Achr2-167660305-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_020981.4(B3GALT1):c.-352+13339G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0587 in 152,074 control chromosomes in the GnomAD database, including 561 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 0.059 (561 hom., cov: 32)
• Consequence: B3GALT1 NM_020981.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0270

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.139 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
B3GALT1	NM_020981.4	c.-352+13339G>A		intron_variant		ENST00000392690.4
B3GALT1	XM_011512085.3	c.-368+13339G>A		intron_variant
B3GALT1	XM_047446159.1	c.-352+13339G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
B3GALT1	ENST00000392690.4	c.-352+13339G>A		intron_variant			NM_020981.4	P1

Frequencies

GnomAD3 genomes AF: 0.0586 AC: 8904 AN: 151956 Hom.: 558 Cov.: 32

Gnomad AFR AF: 0.142

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0863

Gnomad ASJ AF: 0.0193

Gnomad EAS AF: 0.0998

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.00509

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.00699

Gnomad OTH AF: 0.0489

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

GnomAD4 genome AF: 0.0587 AC: 8928 AN: 152074 Hom.: 561 Cov.: 32 AF XY: 0.0593 AC XY: 4406 AN XY: 74350

Gnomad4 AFR AF: 0.142

Gnomad4 AMR AF: 0.0863

Gnomad4 ASJ AF: 0.0193

Gnomad4 EAS AF: 0.0995

Gnomad4 SAS AF: 0.0999

Gnomad4 FIN AF: 0.00509

Gnomad4 NFE AF: 0.00699

Gnomad4 OTH AF: 0.0546

Alfa AF: 0.0125 Hom.: 11

Bravo AF: 0.0679

Asia WGS AF: 0.135 AC: 468 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
Cadd	Benign	11
Dann	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10497327; hg19: chr2-168516815;