15-92403068-G-C

Variant summary

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

The NM_006011.4(ST8SIA2):c.98+8906G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.495 in 151,958 control chromosomes in the GnomAD database, including 18,757 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 0.49 (18757 hom., cov: 31)
• Consequence: ST8SIA2 NM_006011.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0350

Genes affected

ST8SIA2 (HGNC:10870): (ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 2) The protein encoded by this gene is a type II membrane protein that is thought to catalyze the transfer of sialic acid from CMP-sialic acid to N-linked oligosaccharides and glycoproteins. The encoded protein may be found in the Golgi apparatus and may be involved in the production of polysialic acid, a modulator of the adhesive properties of neural cell adhesion molecule (NCAM1). This protein is a member of glycosyltransferase family 29. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.514 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ST8SIA2	NM_006011.4	c.98+8906G>C		intron_variant		ENST00000268164.8
ST8SIA2	NM_001330416.2	c.98+8906G>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ST8SIA2	ENST00000268164.8	c.98+8906G>C		intron_variant		1	NM_006011.4	P1
ST8SIA2	ENST00000539113.5	c.98+8906G>C		intron_variant		1
ST8SIA2	ENST00000555434.1	c.98+8906G>C		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.495 AC: 75131 AN: 151840 Hom.: 18749 Cov.: 31

Gnomad AFR AF: 0.520

Gnomad AMI AF: 0.310

Gnomad AMR AF: 0.523

Gnomad ASJ AF: 0.443

Gnomad EAS AF: 0.468

Gnomad SAS AF: 0.444

Gnomad FIN AF: 0.485

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.485

Gnomad OTH AF: 0.505

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

GnomAD4 genome AF: 0.495 AC: 75187 AN: 151958 Hom.: 18757 Cov.: 31 AF XY: 0.495 AC XY: 36742 AN XY: 74266

Gnomad4 AFR AF: 0.520

Gnomad4 AMR AF: 0.523

Gnomad4 ASJ AF: 0.443

Gnomad4 EAS AF: 0.469

Gnomad4 SAS AF: 0.443

Gnomad4 FIN AF: 0.485

Gnomad4 NFE AF: 0.485

Gnomad4 OTH AF: 0.505

Alfa AF: 0.340 Hom.: 826

Bravo AF: 0.500

Asia WGS AF: 0.480 AC: 1668 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	1.7
Dann	Benign	0.43

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: rs11074067; hg19: chr15-92946298;