15-92403096-T-G

Variant names:

• chr15-92403096-T-G
• rs2035645
• NM_006011.4:c.98+8934T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_006011.4(ST8SIA2):​c.98+8934T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.622 in 151,922 control chromosomes in the GnomAD database, including 29,796 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 0.62 (29796 hom., cov: 31)
• Consequence: ST8SIA2 NM_006011.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.946
• Publications: 6 publications found

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]

ST8SIA2 Gene-Disease associations (from GenCC):

• schizophrenia

  Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.823 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006011.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ST8SIA2	NM_006011.4	MANE Select	c.98+8934T>G		intron	N/A	NP_006002.1
	ST8SIA2	NM_001330416.2		c.98+8934T>G		intron	N/A	NP_001317345.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ST8SIA2	ENST00000268164.8	TSL:1 MANE Select	c.98+8934T>G		intron	N/A	ENSP00000268164.3
	ST8SIA2	ENST00000539113.5	TSL:1	c.98+8934T>G		intron	N/A	ENSP00000437382.1
	ST8SIA2	ENST00000555434.1	TSL:5	c.98+8934T>G		intron	N/A	ENSP00000450851.1

Frequencies

GnomAD3 genomes AF: 0.621 AC: 94333 AN: 151804 Hom.: 29765 Cov.: 31

Gnomad AFR AF: 0.657

Gnomad AMI AF: 0.410

Gnomad AMR AF: 0.713

Gnomad ASJ AF: 0.562

Gnomad EAS AF: 0.843

Gnomad SAS AF: 0.630

Gnomad FIN AF: 0.557

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.577

Gnomad OTH AF: 0.637

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

GnomAD4 genome AF: 0.622 AC: 94421 AN: 151922 Hom.: 29796 Cov.: 31 AF XY: 0.627 AC XY: 46557 AN XY: 74272

African (AFR) AF: 0.657 AC: 27236 AN: 41436

American (AMR) AF: 0.713 AC: 10895 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.562 AC: 1949 AN: 3470

East Asian (EAS) AF: 0.844 AC: 4348 AN: 5154

South Asian (SAS) AF: 0.629 AC: 3027 AN: 4814

European-Finnish (FIN) AF: 0.557 AC: 5872 AN: 10544

Middle Eastern (MID) AF: 0.660 AC: 194 AN: 294

European-Non Finnish (NFE) AF: 0.577 AC: 39186 AN: 67910

Other (OTH) AF: 0.636 AC: 1340 AN: 2108

Alfa AF: 0.595 Hom.: 45256

Bravo AF: 0.636

Asia WGS AF: 0.731 AC: 2537 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.48
DANN	Benign	0.48
PhyloP100		-0.95
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: rs2035645; hg19: chr15-92946326;