rs6922893

chr6-70950408-A-Gchr6-70950408-A-T

Variant summary

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

The NM_080742.3(B3GAT2):c.591+5431T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.714 in 152,006 control chromosomes in the GnomAD database, including 39,033 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 0.71 (39033 hom., cov: 31)
• Consequence: B3GAT2 NM_080742.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.935

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.759 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
B3GAT2	NM_080742.3	c.591+5431T>C		intron_variant		ENST00000230053.11
B3GAT2	XM_047418209.1	c.591+5431T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
B3GAT2	ENST00000230053.11	c.591+5431T>C		intron_variant		1	NM_080742.3	P1
B3GAT2	ENST00000615536.1	c.375+5647T>C		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.714 AC: 108429 AN: 151888 Hom.: 39013 Cov.: 31

Gnomad AFR AF: 0.766

Gnomad AMI AF: 0.682

Gnomad AMR AF: 0.747

Gnomad ASJ AF: 0.853

Gnomad EAS AF: 0.605

Gnomad SAS AF: 0.583

Gnomad FIN AF: 0.614

Gnomad MID AF: 0.759

Gnomad NFE AF: 0.701

Gnomad OTH AF: 0.719

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

GnomAD4 genome AF: 0.714 AC: 108499 AN: 152006 Hom.: 39033 Cov.: 31 AF XY: 0.709 AC XY: 52695 AN XY: 74308

Gnomad4 AFR AF: 0.766

Gnomad4 AMR AF: 0.747

Gnomad4 ASJ AF: 0.853

Gnomad4 EAS AF: 0.605

Gnomad4 SAS AF: 0.583

Gnomad4 FIN AF: 0.614

Gnomad4 NFE AF: 0.701

Gnomad4 OTH AF: 0.715

Alfa AF: 0.711 Hom.: 77936

Bravo AF: 0.733

Asia WGS AF: 0.581 AC: 2021 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	0.61
Dann	Benign	0.49

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: rs6922893; hg19: chr6-71660111;