3-98793981-T-A

Variant names:

• chr3-98793981-T-A
• rs14310
• ENST00000469105.5:n.*1013T>A

Variant summary

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

The ENST00000469105.5(ST3GAL6):​n.*1013T>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.361 in 348,794 control chromosomes in the GnomAD database, including 23,135 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 (9789 hom., cov: 32)
  • Exomes 𝑓: 0.36 (13346 hom.)
• Consequence: ST3GAL6 ENST00000469105.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.253
• Publications: 12 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=-0.55).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.377 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ST3GAL6	NM_001323368.2	c.*220T>A		3_prime_UTR_variant	Exon 10 of 10	ENST00000483910.6	NP_001310297.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ST3GAL6	ENST00000483910.6	c.*220T>A		3_prime_UTR_variant	Exon 10 of 10	1	NM_001323368.2	ENSP00000417376.1

Frequencies

GnomAD3 genomes AF: 0.357 AC: 54268 AN: 152016 Hom.: 9788 Cov.: 32

Gnomad AFR AF: 0.337

Gnomad AMI AF: 0.221

Gnomad AMR AF: 0.341

Gnomad ASJ AF: 0.379

Gnomad EAS AF: 0.219

Gnomad SAS AF: 0.343

Gnomad FIN AF: 0.380

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.381

Gnomad OTH AF: 0.372

GnomAD4 exome AF: 0.364 AC: 71555 AN: 196660 Hom.: 13346 Cov.: 3 AF XY: 0.364 AC XY: 36918 AN XY: 101426

African (AFR) AF: 0.336 AC: 1943 AN: 5784

American (AMR) AF: 0.349 AC: 1926 AN: 5524

Ashkenazi Jewish (ASJ) AF: 0.385 AC: 2911 AN: 7554

East Asian (EAS) AF: 0.194 AC: 3325 AN: 17164

South Asian (SAS) AF: 0.337 AC: 1951 AN: 5784

European-Finnish (FIN) AF: 0.394 AC: 5755 AN: 14610

Middle Eastern (MID) AF: 0.347 AC: 361 AN: 1040

European-Non Finnish (NFE) AF: 0.385 AC: 48562 AN: 126144

Other (OTH) AF: 0.369 AC: 4821 AN: 13056

GnomAD4 genome AF: 0.357 AC: 54291 AN: 152134 Hom.: 9789 Cov.: 32 AF XY: 0.356 AC XY: 26484 AN XY: 74366

African (AFR) AF: 0.336 AC: 13944 AN: 41480

American (AMR) AF: 0.341 AC: 5208 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.379 AC: 1314 AN: 3470

East Asian (EAS) AF: 0.220 AC: 1138 AN: 5184

South Asian (SAS) AF: 0.344 AC: 1658 AN: 4824

European-Finnish (FIN) AF: 0.380 AC: 4024 AN: 10584

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

European-Non Finnish (NFE) AF: 0.381 AC: 25913 AN: 67986

Other (OTH) AF: 0.369 AC: 780 AN: 2116

Alfa AF: 0.279 Hom.: 795

Bravo AF: 0.348

Asia WGS AF: 0.249 AC: 866 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.55
CADD	Benign	12
DANN	Benign	0.84
PhyloP100		-0.25
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: rs14310; hg19: chr3-98512825;