15-92443898-A-G

Variant names:

• chr15-92443898-A-G
• rs3784730
• NM_006011.4:c.549-738A>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.549-738A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.439 in 151,856 control chromosomes in the GnomAD database, including 14,869 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 (14869 hom., cov: 31)
• Consequence: ST8SIA2 NM_006011.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.324
• Publications: 13 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=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.509 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ST8SIA2	NM_006011.4	c.549-738A>G		intron_variant	Intron 4 of 5	ENST00000268164.8	NP_006002.1
ST8SIA2	NM_001330416.2	c.486-738A>G		intron_variant	Intron 3 of 4		NP_001317345.1
ST8SIA2	XM_017022642.2	c.612-738A>G		intron_variant	Intron 4 of 5		XP_016878131.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ST8SIA2	ENST00000268164.8	c.549-738A>G		intron_variant	Intron 4 of 5	1	NM_006011.4	ENSP00000268164.3
ST8SIA2	ENST00000539113.5	c.486-738A>G		intron_variant	Intron 3 of 4	1		ENSP00000437382.1
ST8SIA2	ENST00000555434.1	c.420-738A>G		intron_variant	Intron 3 of 4	5		ENSP00000450851.1
ST8SIA2	ENST00000556382.1	n.319-738A>G		intron_variant	Intron 2 of 2	3

Frequencies

GnomAD3 genomes AF: 0.439 AC: 66675 AN: 151738 Hom.: 14856 Cov.: 31

Gnomad AFR AF: 0.497

Gnomad AMI AF: 0.502

Gnomad AMR AF: 0.377

Gnomad ASJ AF: 0.377

Gnomad EAS AF: 0.286

Gnomad SAS AF: 0.525

Gnomad FIN AF: 0.436

Gnomad MID AF: 0.404

Gnomad NFE AF: 0.427

Gnomad OTH AF: 0.437

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

GnomAD4 genome AF: 0.439 AC: 66716 AN: 151856 Hom.: 14869 Cov.: 31 AF XY: 0.439 AC XY: 32590 AN XY: 74202

African (AFR) AF: 0.497 AC: 20548 AN: 41356

American (AMR) AF: 0.377 AC: 5754 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.377 AC: 1308 AN: 3466

East Asian (EAS) AF: 0.286 AC: 1472 AN: 5146

South Asian (SAS) AF: 0.526 AC: 2532 AN: 4816

European-Finnish (FIN) AF: 0.436 AC: 4592 AN: 10538

Middle Eastern (MID) AF: 0.411 AC: 120 AN: 292

European-Non Finnish (NFE) AF: 0.427 AC: 29010 AN: 67950

Other (OTH) AF: 0.439 AC: 923 AN: 2104

Alfa AF: 0.438 Hom.: 7550

Bravo AF: 0.434

Asia WGS AF: 0.430 AC: 1496 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	0.60
PhyloP100		-0.32
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: rs3784730; hg19: chr15-92987128;