3-98784932-A-G

Variant names:

• chr3-98784932-A-G
• rs999147
• NM_001323368.2:c.336-13A>G

Variant summary

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

The NM_001323368.2(ST3GAL6):​c.336-13A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.363 in 1,602,542 control chromosomes in the GnomAD database, including 107,542 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 0.36 (9795 hom., cov: 32)
  • Exomes 𝑓: 0.36 (97747 hom.)
• Consequence: ST3GAL6 NM_001323368.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.26
• Publications: 17 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=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.378 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ST3GAL6	NM_001323368.2	c.336-13A>G		intron_variant	Intron 5 of 9	ENST00000483910.6	NP_001310297.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ST3GAL6	ENST00000483910.6	c.336-13A>G		intron_variant	Intron 5 of 9	1	NM_001323368.2	ENSP00000417376.1

Frequencies

GnomAD3 genomes AF: 0.357 AC: 54270 AN: 151928 Hom.: 9794 Cov.: 32

Gnomad AFR AF: 0.337

Gnomad AMI AF: 0.221

Gnomad AMR AF: 0.343

Gnomad ASJ AF: 0.378

Gnomad EAS AF: 0.215

Gnomad SAS AF: 0.344

Gnomad FIN AF: 0.380

Gnomad MID AF: 0.366

Gnomad NFE AF: 0.382

Gnomad OTH AF: 0.372

GnomAD2 exomes AF: 0.352 AC: 87671 AN: 248990 AF XY: 0.354

Gnomad AFR exome AF: 0.337

Gnomad AMR exome AF: 0.327

Gnomad ASJ exome AF: 0.385

Gnomad EAS exome AF: 0.212

Gnomad FIN exome AF: 0.389

Gnomad NFE exome AF: 0.376

Gnomad OTH exome AF: 0.353

GnomAD4 exome AF: 0.364 AC: 528188 AN: 1450494 Hom.: 97747 Cov.: 28 AF XY: 0.364 AC XY: 262902 AN XY: 721986

African (AFR) AF: 0.336 AC: 11148 AN: 33182

American (AMR) AF: 0.332 AC: 14658 AN: 44208

Ashkenazi Jewish (ASJ) AF: 0.381 AC: 9896 AN: 25944

East Asian (EAS) AF: 0.198 AC: 7826 AN: 39468

South Asian (SAS) AF: 0.350 AC: 29855 AN: 85334

European-Finnish (FIN) AF: 0.386 AC: 20481 AN: 53082

Middle Eastern (MID) AF: 0.383 AC: 2191 AN: 5728

European-Non Finnish (NFE) AF: 0.372 AC: 410302 AN: 1103648

Other (OTH) AF: 0.364 AC: 21831 AN: 59900

GnomAD4 genome AF: 0.357 AC: 54292 AN: 152048 Hom.: 9795 Cov.: 32 AF XY: 0.356 AC XY: 26475 AN XY: 74298

African (AFR) AF: 0.336 AC: 13946 AN: 41488

American (AMR) AF: 0.342 AC: 5227 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.378 AC: 1312 AN: 3468

East Asian (EAS) AF: 0.215 AC: 1111 AN: 5172

South Asian (SAS) AF: 0.345 AC: 1660 AN: 4812

European-Finnish (FIN) AF: 0.380 AC: 4015 AN: 10558

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.381 AC: 25931 AN: 67972

Other (OTH) AF: 0.369 AC: 778 AN: 2108

Alfa AF: 0.366 Hom.: 18336

Bravo AF: 0.349

Asia WGS AF: 0.247 AC: 861 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.010
DANN	Benign	0.66
PhyloP100		-3.3
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
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: rs999147; hg19: chr3-98503776; COSMIC: COSV54579905; COSMIC: COSV54579905;