Variant rs999147 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000483910.6(ST3GAL6):c.336-13A>G variant causes a splice polypyrimidine tract, 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
ENST00000483910.6 splice_polypyrimidine_tract, intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.26

Variant links:

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 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
ST3GAL6	NM_001323368.2 linkuse as main transcript	c.336-13A>G		splice_polypyrimidine_tract_variant, intron_variant		ENST00000483910.6	NP_001310297.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ST3GAL6	ENST00000483910.6 linkuse as main transcript	c.336-13A>G		splice_polypyrimidine_tract_variant, intron_variant		1	NM_001323368.2	ENSP00000417376	P1	Q9Y274-1

Frequencies

GnomAD3 genomes

AF:

0.357

AC:

54270

AN:

151928

Hom.:

9794

Cov.:

show subpopulations

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

GnomAD3 exomes

AF:

0.352

AC:

87671

AN:

248990

Hom.:

15708

AF XY:

0.354

AC XY:

47556

AN XY:

134454

show subpopulations

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 SAS exome

AF:

0.345

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.:

AF XY:

0.364

AC XY:

262902

AN XY:

721986

show subpopulations

Gnomad4 AFR exome

AF:

0.336

Gnomad4 AMR exome

AF:

0.332

Gnomad4 ASJ exome

AF:

0.381

Gnomad4 EAS exome

AF:

0.198

Gnomad4 SAS exome

AF:

0.350

Gnomad4 FIN exome

AF:

0.386

Gnomad4 NFE exome

AF:

0.372

Gnomad4 OTH exome

AF:

0.364

GnomAD4 genome

AF:

0.357

AC:

54292

AN:

152048

Hom.:

9795

Cov.:

AF XY:

0.356

AC XY:

26475

AN XY:

74298

show subpopulations

Gnomad4 AFR

AF:

0.336

Gnomad4 AMR

AF:

0.342

Gnomad4 ASJ

AF:

0.378

Gnomad4 EAS

AF:

0.215

Gnomad4 SAS

AF:

0.345

Gnomad4 FIN

AF:

0.380

Gnomad4 NFE

AF:

0.381

Gnomad4 OTH

AF:

0.369

Alfa

AF:

0.370

Hom.:

10915

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

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over