dbSNP rs1487982: ST8SIA2:c.842+6753A>G (chr15-92451682-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_006011.4(ST8SIA2):c.842+6753A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.198 in 152,142 control chromosomes in the GnomAD database, including 3,349 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 0.20 ( 3349 hom., cov: 32)

Consequence

ST8SIA2
NM_006011.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.797

Publications

5 publications found

Variant links:

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

ST8SIA2 links:

ENSG00000309186 (HGNC:):

ENSG00000309186 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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 = 0.319 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
ST8SIA2	NM_006011.4 link	c.842+6753A>G	intron_variant	Intron 5 of 5	ENST00000268164.8	NP_006002.1	Q92186B2R9U8
ST8SIA2	NM_001330416.2 link	c.779+6753A>G	intron_variant	Intron 4 of 4		NP_001317345.1	C6G488B2R9U8Q4VAY9
ST8SIA2	XM_017022642.2 link	c.905+6753A>G	intron_variant	Intron 5 of 5		XP_016878131.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
ST8SIA2	ENST00000268164.8 link	c.842+6753A>G	intron_variant	Intron 5 of 5	1	NM_006011.4	ENSP00000268164.3	Q92186
ST8SIA2	ENST00000539113.5 link	c.779+6753A>G	intron_variant	Intron 4 of 4	1		ENSP00000437382.1	C6G488
ST8SIA2	ENST00000555434.1 link	c.713+6753A>G	intron_variant	Intron 4 of 4	5		ENSP00000450851.1	G3V2T1
ENSG00000309186	ENST00000839390.1 link	n.218-6069T>C	intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.198

AC:

30038

AN:

152024

Hom.:

3339

Cov.:

show subpopulations

Gnomad AFR

AF:

0.232

Gnomad AMI

AF:

0.274

Gnomad AMR

AF:

0.326

Gnomad ASJ

AF:

0.133

Gnomad EAS

AF:

0.123

Gnomad SAS

AF:

0.0705

Gnomad FIN

AF:

0.134

Gnomad MID

AF:

0.146

Gnomad NFE

AF:

0.175

Gnomad OTH

AF:

0.185

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

GnomAD4 genome

AF:

0.198

AC:

30077

AN:

152142

Hom.:

3349

Cov.:

AF XY:

0.194

AC XY:

14401

AN XY:

74382

show subpopulations

African (AFR)

AF:

0.232

AC:

9647

AN:

41494

American (AMR)

AF:

0.327

AC:

4993

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.133

AC:

463

AN:

3472

East Asian (EAS)

AF:

0.123

AC:

636

AN:

5156

South Asian (SAS)

AF:

0.0709

AC:

342

AN:

4822

European-Finnish (FIN)

AF:

0.134

AC:

1422

AN:

10598

Middle Eastern (MID)

AF:

0.143

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.175

AC:

11895

AN:

67990

Other (OTH)

AF:

0.183

AC:

387

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1218

2435

3653

4870

6088

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

298

596

894

1192

1490

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.188

Hom.:

5431

Bravo

AF:

0.218

Asia WGS

AF:

0.135

AC:

470

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

2.8

(source)

DANN

Benign

0.37

PhyloP100

0.80

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over