3-98772775-G-T

Position:

• chr3-98772775-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.168-38G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.425 in 1,414,936 control chromosomes in the GnomAD database, including 130,543 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 0.41 (12907 hom., cov: 32)
  • Exomes 𝑓: 0.43 (117636 hom.)
• Consequence: ST3GAL6 NM_001323368.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.22

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]

ST3GAL6 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.445 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ST3GAL6	NM_001323368.2	c.168-38G>T		intron_variant		ENST00000483910.6	NP_001310297.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ST3GAL6	ENST00000483910.6	c.168-38G>T		intron_variant		1	NM_001323368.2	ENSP00000417376.1

Frequencies

GnomAD3 genomes AF: 0.409 AC: 62152 AN: 151928 Hom.: 12890 Cov.: 32

Gnomad AFR AF: 0.385

Gnomad AMI AF: 0.329

Gnomad AMR AF: 0.371

Gnomad ASJ AF: 0.415

Gnomad EAS AF: 0.190

Gnomad SAS AF: 0.355

Gnomad FIN AF: 0.435

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.450

Gnomad OTH AF: 0.412

GnomAD3 exomes AF: 0.395 AC: 98419 AN: 248926 Hom.: 20118 AF XY: 0.397 AC XY: 53402 AN XY: 134656

Gnomad AFR exome AF: 0.389

Gnomad AMR exome AF: 0.343

Gnomad ASJ exome AF: 0.422

Gnomad EAS exome AF: 0.190

Gnomad SAS exome AF: 0.363

Gnomad FIN exome AF: 0.442

Gnomad NFE exome AF: 0.443

Gnomad OTH exome AF: 0.400

GnomAD4 exome AF: 0.427 AC: 539282 AN: 1262890 Hom.: 117636 Cov.: 17 AF XY: 0.425 AC XY: 271705 AN XY: 638890

Gnomad4 AFR exome AF: 0.383

Gnomad4 AMR exome AF: 0.348

Gnomad4 ASJ exome AF: 0.416

Gnomad4 EAS exome AF: 0.176

Gnomad4 SAS exome AF: 0.368

Gnomad4 FIN exome AF: 0.440

Gnomad4 NFE exome AF: 0.448

Gnomad4 OTH exome AF: 0.418

GnomAD4 genome AF: 0.409 AC: 62204 AN: 152046 Hom.: 12907 Cov.: 32 AF XY: 0.407 AC XY: 30270 AN XY: 74316

Gnomad4 AFR AF: 0.385

Gnomad4 AMR AF: 0.370

Gnomad4 ASJ AF: 0.415

Gnomad4 EAS AF: 0.190

Gnomad4 SAS AF: 0.356

Gnomad4 FIN AF: 0.435

Gnomad4 NFE AF: 0.450

Gnomad4 OTH AF: 0.408

Alfa AF: 0.367 Hom.: 2088

Bravo AF: 0.399

Asia WGS AF: 0.260 AC: 905 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.65
DANN	Benign	0.39

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: rs2334230; hg19: chr3-98491619; COSMIC: COSV54581983; COSMIC: COSV54581983;