10-17398396-A-G

Variant names:

• chr10-17398396-A-G
• rs1041216
• NM_001004470.3:c.201-7776T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001004470.3(ST8SIA6):​c.201-7776T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0325 in 152,230 control chromosomes in the GnomAD database, including 84 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 0.033 (84 hom., cov: 32)
• Consequence: ST8SIA6 NM_001004470.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.523
• 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0501 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ST8SIA6	NM_001004470.3	c.201-7776T>C		intron_variant	Intron 2 of 7	ENST00000377602.5	NP_001004470.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ST8SIA6	ENST00000377602.5	c.201-7776T>C		intron_variant	Intron 2 of 7	1	NM_001004470.3	ENSP00000366827.4

Frequencies

GnomAD3 genomes AF: 0.0324 AC: 4936 AN: 152112 Hom.: 83 Cov.: 32

Gnomad AFR AF: 0.0425

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0305

Gnomad ASJ AF: 0.0199

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.0550

Gnomad FIN AF: 0.0190

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0308

Gnomad OTH AF: 0.0292

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

GnomAD4 genome AF: 0.0325 AC: 4949 AN: 152230 Hom.: 84 Cov.: 32 AF XY: 0.0318 AC XY: 2363 AN XY: 74422

African (AFR) AF: 0.0426 AC: 1771 AN: 41552

American (AMR) AF: 0.0306 AC: 468 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0199 AC: 69 AN: 3470

East Asian (EAS) AF: 0.00155 AC: 8 AN: 5172

South Asian (SAS) AF: 0.0555 AC: 268 AN: 4828

European-Finnish (FIN) AF: 0.0190 AC: 202 AN: 10610

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.0308 AC: 2094 AN: 68006

Other (OTH) AF: 0.0289 AC: 61 AN: 2110

Alfa AF: 0.0348 Hom.: 48

Bravo AF: 0.0329

Asia WGS AF: 0.0320 AC: 110 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.12
DANN	Benign	0.61
PhyloP100		-0.52
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: rs1041216; hg19: chr10-17440395;