chr15-92409620-G-A

Position:

• chr15-92409620-G-A

Variant summary

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

The NM_006011.4(ST8SIA2):​c.98+15458G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.44 in 152,042 control chromosomes in the GnomAD database, including 16,150 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 0.44 (16150 hom., cov: 32)
• Consequence: ST8SIA2 NM_006011.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.105

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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.661 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ST8SIA2	NM_006011.4	c.98+15458G>A		intron_variant		ENST00000268164.8
ST8SIA2	XM_017022642.2	c.-3707G>A		5_prime_UTR_variant	1/6
ST8SIA2	NM_001330416.2	c.98+15458G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ST8SIA2	ENST00000268164.8	c.98+15458G>A		intron_variant		1	NM_006011.4	P1
ST8SIA2	ENST00000539113.5	c.98+15458G>A		intron_variant		1
ST8SIA2	ENST00000555434.1	c.98+15458G>A		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.441 AC: 66928 AN: 151924 Hom.: 16148 Cov.: 32

Gnomad AFR AF: 0.242

Gnomad AMI AF: 0.388

Gnomad AMR AF: 0.534

Gnomad ASJ AF: 0.564

Gnomad EAS AF: 0.679

Gnomad SAS AF: 0.501

Gnomad FIN AF: 0.489

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.505

Gnomad OTH AF: 0.444

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

GnomAD4 genome AF: 0.440 AC: 66942 AN: 152042 Hom.: 16150 Cov.: 32 AF XY: 0.446 AC XY: 33115 AN XY: 74294

Gnomad4 AFR AF: 0.241

Gnomad4 AMR AF: 0.535

Gnomad4 ASJ AF: 0.564

Gnomad4 EAS AF: 0.679

Gnomad4 SAS AF: 0.501

Gnomad4 FIN AF: 0.489

Gnomad4 NFE AF: 0.505

Gnomad4 OTH AF: 0.439

Alfa AF: 0.467 Hom.: 2576

Bravo AF: 0.434

Asia WGS AF: 0.518 AC: 1799 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.6
DANN	Benign	0.70

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: rs11637898; hg19: chr15-92952850;