dbSNP rs11074066: ST8SIA2:c.98+7472A>C (chr15-92401634-A-C) – 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.98+7472A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.576 in 152,012 control chromosomes in the GnomAD database, including 25,378 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 0.58 ( 25378 hom., cov: 32)

Consequence

ST8SIA2
NM_006011.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.61

Publications

4 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:

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=-0.95).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.61 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ST8SIA2	NM_006011.4 link	c.98+7472A>C		intron_variant	Intron 1 of 5	ENST00000268164.8	NP_006002.1	Q92186B2R9U8
ST8SIA2	NM_001330416.2 link	c.98+7472A>C		intron_variant	Intron 1 of 4		NP_001317345.1	C6G488B2R9U8Q4VAY9

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
ST8SIA2	ENST00000268164.8 link	c.98+7472A>C	intron_variant	Intron 1 of 5	1	NM_006011.4	ENSP00000268164.3	Q92186
ST8SIA2	ENST00000539113.5 link	c.98+7472A>C	intron_variant	Intron 1 of 4	1		ENSP00000437382.1	C6G488
ST8SIA2	ENST00000555434.1 link	c.98+7472A>C	intron_variant	Intron 1 of 4	5		ENSP00000450851.1	G3V2T1

Frequencies

GnomAD3 genomes

AF:

0.576

AC:

87449

AN:

151892

Hom.:

25363

Cov.:

show subpopulations

Gnomad AFR

AF:

0.617

Gnomad AMI

AF:

0.410

Gnomad AMR

AF:

0.593

Gnomad ASJ

AF:

0.537

Gnomad EAS

AF:

0.525

Gnomad SAS

AF:

0.537

Gnomad FIN

AF:

0.544

Gnomad MID

AF:

0.633

Gnomad NFE

AF:

0.562

Gnomad OTH

AF:

0.593

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

GnomAD4 genome

AF:

0.576

AC:

87520

AN:

152012

Hom.:

25378

Cov.:

AF XY:

0.576

AC XY:

42768

AN XY:

74264

show subpopulations

African (AFR)

AF:

0.617

AC:

25575

AN:

41466

American (AMR)

AF:

0.593

AC:

9061

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.537

AC:

1864

AN:

3470

East Asian (EAS)

AF:

0.526

AC:

2713

AN:

5162

South Asian (SAS)

AF:

0.536

AC:

2580

AN:

4816

European-Finnish (FIN)

AF:

0.544

AC:

5738

AN:

10548

Middle Eastern (MID)

AF:

0.650

AC:

191

AN:

294

European-Non Finnish (NFE)

AF:

0.562

AC:

38174

AN:

67952

Other (OTH)

AF:

0.592

AC:

1250

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1913

3826

5739

7652

9565

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

744

1488

2232

2976

3720

<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:

0.566

Hom.:

92555

Bravo

AF:

0.582

Asia WGS

AF:

0.562

AC:

1952

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

0.10

(source)

DANN

Benign

0.44

PhyloP100

-1.6

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