rs828593

Positions:

• chr3-98743201-C-A
• chr3-98743201-C-G
• chr3-98743201-C-T

Variant summary

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

The ENST00000394162.5(ST3GAL6):​c.-184+10190C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.41 in 150,882 control chromosomes in the GnomAD database, including 12,993 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 0.41 (12993 hom., cov: 28)
• Consequence: ST3GAL6 ENST00000394162.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.540

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=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.535 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ST3GAL6	NM_001271142.2	c.-340+10669C>A		intron_variant			NP_001258071.1
ST3GAL6	NM_001271145.2	c.148+10190C>A		intron_variant			NP_001258074.1
ST3GAL6	NM_001271146.2	c.-12+10669C>A		intron_variant			NP_001258075.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ST3GAL6	ENST00000394162.5	c.-184+10190C>A		intron_variant		1		ENSP00000377717	P1
ST3GAL6	ENST00000613264.5	c.-12+10190C>A		intron_variant		1		ENSP00000480884	P1
ST3GAL6	ENST00000469105.5	c.-12+10669C>A		intron_variant, NMD_transcript_variant		1		ENSP00000419690

Frequencies

GnomAD3 genomes AF: 0.410 AC: 61778 AN: 150770 Hom.: 12987 Cov.: 28

Gnomad AFR AF: 0.336

Gnomad AMI AF: 0.318

Gnomad AMR AF: 0.532

Gnomad ASJ AF: 0.418

Gnomad EAS AF: 0.414

Gnomad SAS AF: 0.554

Gnomad FIN AF: 0.387

Gnomad MID AF: 0.577

Gnomad NFE AF: 0.419

Gnomad OTH AF: 0.432

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

GnomAD4 genome AF: 0.410 AC: 61821 AN: 150882 Hom.: 12993 Cov.: 28 AF XY: 0.412 AC XY: 30390 AN XY: 73678

Gnomad4 AFR AF: 0.336

Gnomad4 AMR AF: 0.532

Gnomad4 ASJ AF: 0.418

Gnomad4 EAS AF: 0.415

Gnomad4 SAS AF: 0.552

Gnomad4 FIN AF: 0.387

Gnomad4 NFE AF: 0.419

Gnomad4 OTH AF: 0.435

Alfa AF: 0.407 Hom.: 1619

Bravo AF: 0.414

Asia WGS AF: 0.444 AC: 1541 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.28
DANN	Benign	0.11

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: rs828593; hg19: chr3-98462045;