10-17346144-C-T

Position:

• chr10-17346144-C-T

Variant summary

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

The ENST00000377602.5(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 ENST00000377602.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.288

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=-0.68).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.395 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ST8SIA6	NM_001004470.3	c.377+13370G>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.377+13370G>A		intron_variant		1	NM_001004470.3	ENSP00000366827	P1
ST8SIA6	ENST00000648997.1	c.*119+13370G>A		intron_variant, NMD_transcript_variant				ENSP00000497856

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

Gnomad4 AFR AF: 0.00457

Gnomad4 AMR AF: 0.156

Gnomad4 ASJ AF: 0.00202

Gnomad4 EAS AF: 0.410

Gnomad4 SAS AF: 0.0191

Gnomad4 FIN AF: 0.112

Gnomad4 NFE AF: 0.00369

Gnomad4 OTH AF: 0.0463

Alfa AF: 0.0283 Hom.: 910

Bravo AF: 0.0475

Asia WGS AF: 0.159 AC: 551 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	6.4
DANN	Benign	0.83

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: rs359312; hg19: chr10-17388143;