NM_001004470.3:c.290+3756G>A

Variant names:

• chr10-17386775-C-T
• rs371210
• NM_001004470.3:c.290+3756G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 publications found

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]

ST8SIA6-AS1 (HGNC:44880): (ST8SIA6 antisense RNA 1)

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 = 0.621 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001004470.3. 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
	ST8SIA6	NM_001004470.3	MANE Select	c.290+3756G>A		intron	N/A	NP_001004470.1
	ST8SIA6	NM_001345961.2		c.-233+3756G>A		intron	N/A	NP_001332890.1
	ST8SIA6	NR_144322.2		n.630+3756G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ST8SIA6	ENST00000377602.5	TSL:1 MANE Select	c.290+3756G>A		intron	N/A	ENSP00000366827.4
	ST8SIA6	ENST00000648997.1		n.230+3756G>A		intron	N/A	ENSP00000497856.1
	ST8SIA6-AS1	ENST00000457649.7	TSL:1	n.-137C>T		upstream_gene	N/A

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

African (AFR) AF: 0.331 AC: 13700 AN: 41396

American (AMR) AF: 0.378 AC: 5767 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.166 AC: 577 AN: 3470

East Asian (EAS) AF: 0.640 AC: 3250 AN: 5082

South Asian (SAS) AF: 0.284 AC: 1368 AN: 4818

European-Finnish (FIN) AF: 0.417 AC: 4395 AN: 10528

Middle Eastern (MID) AF: 0.216 AC: 63 AN: 292

European-Non Finnish (NFE) AF: 0.263 AC: 17871 AN: 67860

Other (OTH) AF: 0.270 AC: 569 AN: 2108

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.2
DANN	Benign	0.40
PhyloP100		-0.92
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: rs371210; hg19: chr10-17428774;