rs371210

Positions:

• chr10-17386775-C-T

Variant summary

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

The NM_001004470.3(ST8SIA6):​c.290+3756G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.315 in 151,698 control chromosomes in the GnomAD database, including 8,119 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 0.32 (8119 hom., cov: 31)
• Consequence: ST8SIA6 NM_001004470.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.921

Genes affected

ST8SIA6 (HGNC:23317): (ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 6) This gene encodes a member of the glycosyltransferase 29 protein family. Members of this protein family synthesize sialylglycoconjugates. Sialylation may contribute to multidrug resistance in cancer cells. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2016]

ACMG classification

Verdict is Benign. Variant got -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 = 0.621 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ST8SIA6	NM_001004470.3	c.290+3756G>A		intron_variant		ENST00000377602.5	NP_001004470.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ST8SIA6	ENST00000377602.5	c.290+3756G>A		intron_variant		1	NM_001004470.3	ENSP00000366827	P1
ST8SIA6	ENST00000648997.1	c.231+3756G>A		intron_variant, NMD_transcript_variant				ENSP00000497856

Frequencies

GnomAD3 genomes AF: 0.315 AC: 47712 AN: 151580 Hom.: 8096 Cov.: 31

Gnomad AFR AF: 0.330

Gnomad AMI AF: 0.251

Gnomad AMR AF: 0.378

Gnomad ASJ AF: 0.166

Gnomad EAS AF: 0.640

Gnomad SAS AF: 0.284

Gnomad FIN AF: 0.417

Gnomad MID AF: 0.204

Gnomad NFE AF: 0.263

Gnomad OTH AF: 0.272

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

GnomAD4 genome AF: 0.315 AC: 47787 AN: 151698 Hom.: 8119 Cov.: 31 AF XY: 0.326 AC XY: 24146 AN XY: 74098

Gnomad4 AFR AF: 0.331

Gnomad4 AMR AF: 0.378

Gnomad4 ASJ AF: 0.166

Gnomad4 EAS AF: 0.640

Gnomad4 SAS AF: 0.284

Gnomad4 FIN AF: 0.417

Gnomad4 NFE AF: 0.263

Gnomad4 OTH AF: 0.270

Alfa AF: 0.312 Hom.: 965

Bravo AF: 0.316

Asia WGS AF: 0.430 AC: 1493 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.2
DANN	Benign	0.40

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: rs371210; hg19: chr10-17428774;