3-98785833-A-T

Variant names:

• chr3-98785833-A-T
• rs828609
• NM_001323368.2:c.431+793A>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.431+793A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.541 in 151,986 control chromosomes in the GnomAD database, including 22,544 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 0.54 (22544 hom., cov: 32)
• Consequence: ST3GAL6 NM_001323368.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.498
• Publications: 2 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.762 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001323368.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ST3GAL6	NM_001323368.2	MANE Select	c.431+793A>T		intron	N/A	NP_001310297.1
	ST3GAL6	NM_001271145.2		c.590+793A>T		intron	N/A	NP_001258074.1
	ST3GAL6	NM_001271146.2		c.431+793A>T		intron	N/A	NP_001258075.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ST3GAL6	ENST00000483910.6	TSL:1 MANE Select	c.431+793A>T		intron	N/A	ENSP00000417376.1
	ST3GAL6	ENST00000394162.5	TSL:1	c.431+793A>T		intron	N/A	ENSP00000377717.1
	ST3GAL6	ENST00000613264.5	TSL:1	c.431+793A>T		intron	N/A	ENSP00000480884.2

Frequencies

GnomAD3 genomes AF: 0.541 AC: 82160 AN: 151868 Hom.: 22531 Cov.: 32

Gnomad AFR AF: 0.458

Gnomad AMI AF: 0.659

Gnomad AMR AF: 0.600

Gnomad ASJ AF: 0.587

Gnomad EAS AF: 0.782

Gnomad SAS AF: 0.642

Gnomad FIN AF: 0.563

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.545

Gnomad OTH AF: 0.546

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

GnomAD4 genome AF: 0.541 AC: 82194 AN: 151986 Hom.: 22544 Cov.: 32 AF XY: 0.544 AC XY: 40449 AN XY: 74292

African (AFR) AF: 0.457 AC: 18960 AN: 41450

American (AMR) AF: 0.600 AC: 9166 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.587 AC: 2035 AN: 3466

East Asian (EAS) AF: 0.782 AC: 4035 AN: 5158

South Asian (SAS) AF: 0.641 AC: 3091 AN: 4820

European-Finnish (FIN) AF: 0.563 AC: 5937 AN: 10548

Middle Eastern (MID) AF: 0.602 AC: 177 AN: 294

European-Non Finnish (NFE) AF: 0.545 AC: 37032 AN: 67962

Other (OTH) AF: 0.550 AC: 1161 AN: 2110

Alfa AF: 0.528 Hom.: 2669

Bravo AF: 0.544

Asia WGS AF: 0.717 AC: 2492 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.65
DANN	Benign	0.49
PhyloP100		-0.50
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: rs828609; hg19: chr3-98504677;