rs2460691

Variant names:

• chr6-70904152-G-C
• rs2460691
• NM_080742.3:c.592-9880C>G

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_080742.3. 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
	B3GAT2	NM_080742.3	MANE Select	c.592-9880C>G		intron	N/A	NP_542780.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	B3GAT2	ENST00000230053.11	TSL:1 MANE Select	c.592-9880C>G		intron	N/A	ENSP00000230053.6
	B3GAT2	ENST00000615536.1	TSL:1	c.376-9880C>G		intron	N/A	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

African (AFR) AF: 0.547 AC: 22662 AN: 41392

American (AMR) AF: 0.555 AC: 8481 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.508 AC: 1758 AN: 3464

East Asian (EAS) AF: 0.657 AC: 3386 AN: 5156

South Asian (SAS) AF: 0.417 AC: 2006 AN: 4814

European-Finnish (FIN) AF: 0.311 AC: 3279 AN: 10544

Middle Eastern (MID) AF: 0.429 AC: 126 AN: 294

European-Non Finnish (NFE) AF: 0.372 AC: 25307 AN: 67942

Other (OTH) AF: 0.473 AC: 999 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.14
DANN	Benign	0.40
PhyloP100		-1.5
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2460691; hg19: chr6-71613855;