NM_001004470.3:c.200+31193A>T

Variant names:

• chr10-17422366-T-A
• rs10508529
• NM_001004470.3:c.200+31193A>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_001004470.3(ST8SIA6):​c.200+31193A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0745 in 152,246 control chromosomes in the GnomAD database, including 1,205 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 0.074 (1205 hom., cov: 32)
• Consequence: ST8SIA6 NM_001004470.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.386
• Publications: 1 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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.27).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.234 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.200+31193A>T		intron	N/A	NP_001004470.1
	ST8SIA6	NM_001345961.2		c.-323+31193A>T		intron	N/A	NP_001332890.1
	ST8SIA6	NR_144322.2		n.540+31193A>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ST8SIA6	ENST00000377602.5	TSL:1 MANE Select	c.200+31193A>T		intron	N/A	ENSP00000366827.4
	ST8SIA6	ENST00000648997.1		n.140+31193A>T		intron	N/A	ENSP00000497856.1
	ST8SIA6-AS1	ENST00000657045.1		n.515+14122T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0742 AC: 11295 AN: 152128 Hom.: 1195 Cov.: 32

Gnomad AFR AF: 0.238

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0349

Gnomad ASJ AF: 0.0294

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00228

Gnomad FIN AF: 0.0147

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.00726

Gnomad OTH AF: 0.0641

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

GnomAD4 genome AF: 0.0745 AC: 11338 AN: 152246 Hom.: 1205 Cov.: 32 AF XY: 0.0716 AC XY: 5330 AN XY: 74436

African (AFR) AF: 0.238 AC: 9893 AN: 41520

American (AMR) AF: 0.0348 AC: 533 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0294 AC: 102 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5190

South Asian (SAS) AF: 0.00228 AC: 11 AN: 4820

European-Finnish (FIN) AF: 0.0147 AC: 156 AN: 10604

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.00725 AC: 493 AN: 68026

Other (OTH) AF: 0.0639 AC: 135 AN: 2114

Alfa AF: 0.0484 Hom.: 88

Bravo AF: 0.0833

Asia WGS AF: 0.0150 AC: 54 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.27
CADD	Benign	8.7
DANN	Benign	0.76
PhyloP100		-0.39
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: rs10508529; hg19: chr10-17464365;