rs278390

Positions:

• chr3-98790743-G-A
• chr3-98790743-G-T

Variant summary

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

The NM_001323368.2(ST3GAL6):​c.757-1098G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.309 in 151,876 control chromosomes in the GnomAD database, including 8,702 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 0.31 (8702 hom., cov: 31)
• Consequence: ST3GAL6 NM_001323368.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.766

Genes affected

ST3GAL6 (HGNC:18080): (ST3 beta-galactoside alpha-2,3-sialyltransferase 6) The protein encoded by this gene is a member of the sialyltransferase family. Members of this family are enzymes that transfer sialic acid from the activated cytidine 5'-monophospho-N-acetylneuraminic acid to terminal positions on sialylated glycolipids (gangliosides) or to the N- or O-linked sugar chains of glycoproteins. This protein has high specificity for neolactotetraosylceramide and neolactohexaosylceramide as glycolipid substrates and may contribute to the formation of selectin ligands and sialyl Lewis X, a carbohydrate important for cell-to-cell recognition and a blood group antigen. [provided by RefSeq, Apr 2016]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.687 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ST3GAL6	NM_001323368.2	c.757-1098G>A		intron_variant		ENST00000483910.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ST3GAL6	ENST00000483910.6	c.757-1098G>A		intron_variant		1	NM_001323368.2	P1

Frequencies

GnomAD3 genomes AF: 0.310 AC: 46984 AN: 151758 Hom.: 8699 Cov.: 31

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.302

Gnomad AMR AF: 0.439

Gnomad ASJ AF: 0.345

Gnomad EAS AF: 0.706

Gnomad SAS AF: 0.416

Gnomad FIN AF: 0.372

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.344

Gnomad OTH AF: 0.341

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

GnomAD4 genome AF: 0.309 AC: 46998 AN: 151876 Hom.: 8702 Cov.: 31 AF XY: 0.315 AC XY: 23391 AN XY: 74230

Gnomad4 AFR AF: 0.122

Gnomad4 AMR AF: 0.439

Gnomad4 ASJ AF: 0.345

Gnomad4 EAS AF: 0.706

Gnomad4 SAS AF: 0.415

Gnomad4 FIN AF: 0.372

Gnomad4 NFE AF: 0.344

Gnomad4 OTH AF: 0.343

Alfa AF: 0.352 Hom.: 12996

Bravo AF: 0.310

Asia WGS AF: 0.535 AC: 1857 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.32
DANN	Benign	0.52

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		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: rs278390; hg19: chr3-98509587;