3-98774287-C-T

Variant names:

• chr3-98774287-C-T
• rs278376
• NM_001323368.2:c.335+304C>T

Variant summary

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

The NM_001323368.2(ST3GAL6):​c.335+304C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.327 in 152,024 control chromosomes in the GnomAD database, including 9,332 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 0.33 (9332 hom., cov: 32)
• Consequence: ST3GAL6 NM_001323368.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.240
• Publications: 5 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=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.716 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ST3GAL6	NM_001323368.2	c.335+304C>T		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.335+304C>T		intron_variant	Intron 5 of 9	1	NM_001323368.2	ENSP00000417376.1

Frequencies

GnomAD3 genomes AF: 0.328 AC: 49771 AN: 151906 Hom.: 9332 Cov.: 32

Gnomad AFR AF: 0.171

Gnomad AMI AF: 0.314

Gnomad AMR AF: 0.452

Gnomad ASJ AF: 0.348

Gnomad EAS AF: 0.736

Gnomad SAS AF: 0.418

Gnomad FIN AF: 0.373

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.349

Gnomad OTH AF: 0.361

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

GnomAD4 genome AF: 0.327 AC: 49783 AN: 152024 Hom.: 9332 Cov.: 32 AF XY: 0.333 AC XY: 24708 AN XY: 74306

African (AFR) AF: 0.171 AC: 7076 AN: 41490

American (AMR) AF: 0.453 AC: 6921 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.348 AC: 1204 AN: 3464

East Asian (EAS) AF: 0.735 AC: 3797 AN: 5164

South Asian (SAS) AF: 0.418 AC: 2013 AN: 4818

European-Finnish (FIN) AF: 0.373 AC: 3938 AN: 10560

Middle Eastern (MID) AF: 0.344 AC: 101 AN: 294

European-Non Finnish (NFE) AF: 0.349 AC: 23684 AN: 67940

Other (OTH) AF: 0.362 AC: 763 AN: 2108

Alfa AF: 0.344 Hom.: 5612

Bravo AF: 0.330

Asia WGS AF: 0.547 AC: 1900 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	4.2
DANN	Benign	0.59
PhyloP100		0.24
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: rs278376; hg19: chr3-98493131;