10-17346144-C-T

Variant names:

• chr10-17346144-C-T
• rs359312
• NM_001004470.3:c.377+13370G>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.377+13370G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0416 in 152,266 control chromosomes in the GnomAD database, including 748 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 0.042 (748 hom., cov: 32)
• Consequence: ST8SIA6 NM_001004470.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.288
• Publications: 12 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]

ENSG00000303005 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.395 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ST8SIA6	NM_001004470.3	MANE Select	c.377+13370G>A		intron	N/A	NP_001004470.1	P61647
	ST8SIA6	NM_001345961.2		c.-77+13370G>A		intron	N/A	NP_001332890.1
	ST8SIA6	NR_144322.2		n.717+13370G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ST8SIA6	ENST00000377602.5	TSL:1 MANE Select	c.377+13370G>A		intron	N/A	ENSP00000366827.4	P61647
	ST8SIA6	ENST00000648997.1		n.*119+13370G>A		intron	N/A	ENSP00000497856.1	A0A3B3ITM3
	ENSG00000303005	ENST00000790990.1		n.111-2824C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0415 AC: 6317 AN: 152148 Hom.: 747 Cov.: 32

Gnomad AFR AF: 0.00458

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.156

Gnomad ASJ AF: 0.00202

Gnomad EAS AF: 0.410

Gnomad SAS AF: 0.0193

Gnomad FIN AF: 0.112

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00369

Gnomad OTH AF: 0.0435

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

GnomAD4 genome AF: 0.0416 AC: 6331 AN: 152266 Hom.: 748 Cov.: 32 AF XY: 0.0516 AC XY: 3844 AN XY: 74434

African (AFR) AF: 0.00457 AC: 190 AN: 41572

American (AMR) AF: 0.156 AC: 2392 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.00202 AC: 7 AN: 3472

East Asian (EAS) AF: 0.410 AC: 2114 AN: 5156

South Asian (SAS) AF: 0.0191 AC: 92 AN: 4824

European-Finnish (FIN) AF: 0.112 AC: 1187 AN: 10590

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.00369 AC: 251 AN: 68036

Other (OTH) AF: 0.0463 AC: 98 AN: 2116

Alfa AF: 0.0274 Hom.: 1144

Bravo AF: 0.0475

Asia WGS AF: 0.159 AC: 551 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	6.4
DANN	Benign	0.83
PhyloP100		0.29
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: rs359312; hg19: chr10-17388143;