chr15-92407653-G-A

Position:

• chr15-92407653-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+13491G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.397 in 152,024 control chromosomes in the GnomAD database, including 12,796 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 0.40 (12796 hom., cov: 32)
• Consequence: ST8SIA2 NM_006011.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.438

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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.585 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ST8SIA2	NM_006011.4	c.98+13491G>A		intron_variant		ENST00000268164.8	NP_006002.1
ST8SIA2	NM_001330416.2	c.98+13491G>A		intron_variant			NP_001317345.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ST8SIA2	ENST00000268164.8	c.98+13491G>A		intron_variant		1	NM_006011.4	ENSP00000268164	P1
ST8SIA2	ENST00000539113.5	c.98+13491G>A		intron_variant		1		ENSP00000437382
ST8SIA2	ENST00000555434.1	c.98+13491G>A		intron_variant		5		ENSP00000450851

Frequencies

GnomAD3 genomes AF: 0.397 AC: 60291 AN: 151906 Hom.: 12789 Cov.: 32

Gnomad AFR AF: 0.253

Gnomad AMI AF: 0.334

Gnomad AMR AF: 0.486

Gnomad ASJ AF: 0.407

Gnomad EAS AF: 0.602

Gnomad SAS AF: 0.406

Gnomad FIN AF: 0.471

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.436

Gnomad OTH AF: 0.406

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

GnomAD4 genome AF: 0.397 AC: 60319 AN: 152024 Hom.: 12796 Cov.: 32 AF XY: 0.403 AC XY: 29975 AN XY: 74320

Gnomad4 AFR AF: 0.253

Gnomad4 AMR AF: 0.486

Gnomad4 ASJ AF: 0.407

Gnomad4 EAS AF: 0.603

Gnomad4 SAS AF: 0.404

Gnomad4 FIN AF: 0.471

Gnomad4 NFE AF: 0.436

Gnomad4 OTH AF: 0.401

Alfa AF: 0.405 Hom.: 6619

Bravo AF: 0.391

Asia WGS AF: 0.451 AC: 1565 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.3
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: rs4777973; hg19: chr15-92950883;