dbSNP rs4762896: ST8SIA1:c.584+29G>A (chr12-22248977-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_003034.4(ST8SIA1):c.584+29G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.221 in 1,527,574 control chromosomes in the GnomAD database, including 39,008 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 0.22 ( 3701 hom., cov: 32)

Exomes 𝑓: 0.22 ( 35307 hom. )

Consequence

ST8SIA1
NM_003034.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0440

Publications

8 publications found

Variant links:

Genes affected

ST8SIA1 (HGNC:10869): (ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 1) Gangliosides are membrane-bound glycosphingolipids containing sialic acid. Ganglioside GD3 is known to be important for cell adhesion and growth of cultured malignant cells. The protein encoded by this gene is a type II membrane protein that catalyzes the transfer of sialic acid from CMP-sialic acid to GM3 to produce gangliosides GD3 and GT3. The encoded protein may be found in the Golgi apparatus and is a member of glycosyltransferase family 29. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Jan 2015]

ST8SIA1 links:

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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=-0.8).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.254 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ST8SIA1	NM_003034.4 link	c.584+29G>A		intron_variant	Intron 4 of 4	ENST00000396037.9	NP_003025.1	Q92185-1
ST8SIA1	NM_001304450.2 link	c.155+29G>A		intron_variant	Intron 3 of 3		NP_001291379.1	Q92185

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ST8SIA1	ENST00000396037.9 link	c.584+29G>A		intron_variant	Intron 4 of 4	1	NM_003034.4	ENSP00000379353.3		Q92185-1

Frequencies

GnomAD3 genomes

AF:

0.215

AC:

32700

AN:

151878

Hom.:

3696

Cov.:

show subpopulations

Gnomad AFR

AF:

0.202

Gnomad AMI

AF:

0.201

Gnomad AMR

AF:

0.261

Gnomad ASJ

AF:

0.301

Gnomad EAS

AF:

0.0620

Gnomad SAS

AF:

0.191

Gnomad FIN

AF:

0.131

Gnomad MID

AF:

0.309

Gnomad NFE

AF:

0.234

Gnomad OTH

AF:

0.244

GnomAD2 exomes

AF:

0.209

AC:

51345

AN:

246026

AF XY:

0.212

show subpopulations

Gnomad AFR exome

AF:

0.202

Gnomad AMR exome

AF:

0.226

Gnomad ASJ exome

AF:

0.307

Gnomad EAS exome

AF:

0.0517

Gnomad FIN exome

AF:

0.134

Gnomad NFE exome

AF:

0.236

Gnomad OTH exome

AF:

0.237

GnomAD4 exome

AF:

0.222

AC:

305235

AN:

1375572

Hom.:

35307

Cov.:

AF XY:

0.223

AC XY:

153626

AN XY:

688972

show subpopulations

African (AFR)

AF:

0.205

AC:

6467

AN:

31622

American (AMR)

AF:

0.227

AC:

9939

AN:

43806

Ashkenazi Jewish (ASJ)

AF:

0.305

AC:

7774

AN:

25494

East Asian (EAS)

AF:

0.0747

AC:

2929

AN:

39198

South Asian (SAS)

AF:

0.201

AC:

16725

AN:

83056

European-Finnish (FIN)

AF:

0.141

AC:

7484

AN:

53160

Middle Eastern (MID)

AF:

0.318

AC:

1786

AN:

5612

European-Non Finnish (NFE)

AF:

0.230

AC:

238768

AN:

1036140

Other (OTH)

AF:

0.232

AC:

13363

AN:

57484

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

11240

22480

33721

44961

56201

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

7854

15708

23562

31416

39270

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.215

AC:

32713

AN:

152002

Hom.:

3701

Cov.:

AF XY:

0.209

AC XY:

15528

AN XY:

74288

show subpopulations

African (AFR)

AF:

0.202

AC:

8365

AN:

41448

American (AMR)

AF:

0.260

AC:

3974

AN:

15264

Ashkenazi Jewish (ASJ)

AF:

0.301

AC:

1044

AN:

3470

East Asian (EAS)

AF:

0.0615

AC:

318

AN:

5168

South Asian (SAS)

AF:

0.191

AC:

918

AN:

4812

European-Finnish (FIN)

AF:

0.131

AC:

1385

AN:

10558

Middle Eastern (MID)

AF:

0.301

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.234

AC:

15916

AN:

67968

Other (OTH)

AF:

0.247

AC:

522

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

1317

2634

3950

5267

6584

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

354

708

1062

1416

1770

<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:

0.240

Hom.:

6147

Bravo

AF:

0.225

Asia WGS

AF:

0.155

AC:

540

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

6.9

(source)

DANN

Benign

0.74

PhyloP100

-0.044

PromoterAI

-0.017

Neutral

(source)

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

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over