rs2460691

Positions:

• chr6-70904152-G-C
• chr6-70904152-G-T

Variant summary

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

The NM_080742.3(B3GAT2):​c.592-9880C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.449 in 151,898 control chromosomes in the GnomAD database, including 16,012 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 0.45 (16012 hom., cov: 31)
• Consequence: B3GAT2 NM_080742.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.46

Genes affected

B3GAT2 (HGNC:922): (beta-1,3-glucuronyltransferase 2) The product of this gene is a transmembrane protein belonging to the glucuronyltransferase family, and catalyzes the transfer of a beta-1,3 linked glucuronic acid to a terminal galactose in different glycoproteins or glycolipids containing a Gal-beta-1-4GlcNAc or Gal-beta-1-3GlcNAc residue. The encoded protein is involved in the synthesis of the human natural killer-1 (HNK-1) carbohydrate epitope, a sulfated trisaccharide implicated in cellular migration and adhesion in the nervous system. [provided by RefSeq, Jul 2008]

LOC105377850 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.638 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
B3GAT2	NM_080742.3	c.592-9880C>G		intron_variant		ENST00000230053.11	NP_542780.1
B3GAT2	XM_047418209.1	c.592-9880C>G		intron_variant			XP_047274165.1
LOC105377850	XR_001744196.2	n.176-343G>C		intron_variant
LOC105377850	XR_942676.3	n.471-343G>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
B3GAT2	ENST00000230053.11	c.592-9880C>G		intron_variant		1	NM_080742.3	ENSP00000230053.6
B3GAT2	ENST00000615536.1	c.376-9880C>G		intron_variant		1		ENSP00000481320.1

Frequencies

GnomAD3 genomes AF: 0.449 AC: 68172 AN: 151782 Hom.: 15984 Cov.: 31

Gnomad AFR AF: 0.548

Gnomad AMI AF: 0.259

Gnomad AMR AF: 0.555

Gnomad ASJ AF: 0.508

Gnomad EAS AF: 0.658

Gnomad SAS AF: 0.416

Gnomad FIN AF: 0.311

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.372

Gnomad OTH AF: 0.476

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

GnomAD4 genome AF: 0.449 AC: 68240 AN: 151898 Hom.: 16012 Cov.: 31 AF XY: 0.449 AC XY: 33352 AN XY: 74234

Gnomad4 AFR AF: 0.547

Gnomad4 AMR AF: 0.555

Gnomad4 ASJ AF: 0.508

Gnomad4 EAS AF: 0.657

Gnomad4 SAS AF: 0.417

Gnomad4 FIN AF: 0.311

Gnomad4 NFE AF: 0.372

Gnomad4 OTH AF: 0.473

Alfa AF: 0.166 Hom.: 246

Bravo AF: 0.479

Asia WGS AF: 0.510 AC: 1774 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.14
DANN	Benign	0.40

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs2460691; hg19: chr6-71613855;