3-98772775-G-T

Variant names:

• chr3-98772775-G-T
• rs2334230
• NM_001323368.2:c.168-38G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001271145.2(ST3GAL6):​c.327-38G>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_001271145.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.22
• Publications: 8 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001271145.2. 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
	ST3GAL6	NM_001323368.2	MANE Select	c.168-38G>T		intron	N/A	NP_001310297.1
	ST3GAL6	NM_001271145.2		c.327-38G>T		intron	N/A	NP_001258074.1
	ST3GAL6	NM_001271146.2		c.168-38G>T		intron	N/A	NP_001258075.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ST3GAL6	ENST00000483910.6	TSL:1 MANE Select	c.168-38G>T		intron	N/A	ENSP00000417376.1
	ST3GAL6	ENST00000394162.5	TSL:1	c.168-38G>T		intron	N/A	ENSP00000377717.1
	ST3GAL6	ENST00000613264.5	TSL:1	c.168-38G>T		intron	N/A	ENSP00000480884.2

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

GnomAD2 exomes AF: 0.395 AC: 98419 AN: 248926 AF XY: 0.397

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 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

African (AFR) AF: 0.383 AC: 11301 AN: 29478

American (AMR) AF: 0.348 AC: 15291 AN: 43972

Ashkenazi Jewish (ASJ) AF: 0.416 AC: 10292 AN: 24722

East Asian (EAS) AF: 0.176 AC: 6795 AN: 38518

South Asian (SAS) AF: 0.368 AC: 29936 AN: 81368

European-Finnish (FIN) AF: 0.440 AC: 23238 AN: 52822

Middle Eastern (MID) AF: 0.402 AC: 2173 AN: 5404

European-Non Finnish (NFE) AF: 0.448 AC: 417812 AN: 932944

Other (OTH) AF: 0.418 AC: 22444 AN: 53662

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

African (AFR) AF: 0.385 AC: 15978 AN: 41464

American (AMR) AF: 0.370 AC: 5660 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.415 AC: 1440 AN: 3466

East Asian (EAS) AF: 0.190 AC: 984 AN: 5174

South Asian (SAS) AF: 0.356 AC: 1714 AN: 4818

European-Finnish (FIN) AF: 0.435 AC: 4598 AN: 10572

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.450 AC: 30550 AN: 67954

Other (OTH) AF: 0.408 AC: 863 AN: 2114

Alfa AF: 0.368 Hom.: 2150

Bravo AF: 0.399

Asia WGS AF: 0.260 AC: 905 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.65
DANN	Benign	0.39
PhyloP100		-1.2
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: rs2334230; hg19: chr3-98491619; COSMIC: COSV54581983; COSMIC: COSV54581983;