chr3-98775816-C-G

Position:

• chr3-98775816-C-G

Variant summary

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

The NM_001323368.2(ST3GAL6):​c.335+1833C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.342 in 152,062 control chromosomes in the GnomAD database, including 9,085 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 0.34 (9085 hom., cov: 32)
• Consequence: ST3GAL6 NM_001323368.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.752

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=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.374 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ST3GAL6	NM_001323368.2	c.335+1833C>G		intron_variant		ENST00000483910.6	NP_001310297.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ST3GAL6	ENST00000483910.6	c.335+1833C>G		intron_variant		1	NM_001323368.2	ENSP00000417376.1

Frequencies

GnomAD3 genomes AF: 0.342 AC: 52010 AN: 151944 Hom.: 9086 Cov.: 32

Gnomad AFR AF: 0.294

Gnomad AMI AF: 0.209

Gnomad AMR AF: 0.331

Gnomad ASJ AF: 0.378

Gnomad EAS AF: 0.214

Gnomad SAS AF: 0.343

Gnomad FIN AF: 0.380

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.378

Gnomad OTH AF: 0.354

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

GnomAD4 genome AF: 0.342 AC: 52033 AN: 152062 Hom.: 9085 Cov.: 32 AF XY: 0.342 AC XY: 25458 AN XY: 74348

Gnomad4 AFR AF: 0.294

Gnomad4 AMR AF: 0.331

Gnomad4 ASJ AF: 0.378

Gnomad4 EAS AF: 0.214

Gnomad4 SAS AF: 0.343

Gnomad4 FIN AF: 0.380

Gnomad4 NFE AF: 0.377

Gnomad4 OTH AF: 0.351

Alfa AF: 0.259 Hom.: 674

Bravo AF: 0.331

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	0.51
DANN	Benign	0.68

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: rs3755574; hg19: chr3-98494660;