dbSNP rs4762737: ST8SIA1:c.*1303C>T (chr12-22200249-G-A) – 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.*1303C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.773 in 152,028 control chromosomes in the GnomAD database, including 45,659 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 0.77 ( 45658 hom., cov: 31)

Exomes 𝑓: 1.0 ( 1 hom. )

Consequence

ST8SIA1
NM_003034.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.33

Publications

3 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:

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=-0.9).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.909 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ST8SIA1	NM_003034.4 link	c.*1303C>T		3_prime_UTR_variant	Exon 5 of 5	ENST00000396037.9	NP_003025.1	Q92185-1
ST8SIA1	NM_001304450.2 link	c.*1303C>T		3_prime_UTR_variant	Exon 4 of 4		NP_001291379.1	Q92185

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
ST8SIA1	ENST00000396037.9 link	c.*1303C>T	3_prime_UTR_variant	Exon 5 of 5	1	NM_003034.4	ENSP00000379353.3	Q92185-1
ST8SIA1	ENST00000544732.5 link	n.151+48757C>T	intron_variant	Intron 2 of 5	5
ST8SIA1	ENST00000545524.5 link	n.249+48757C>T	intron_variant	Intron 3 of 4	3

Frequencies

GnomAD3 genomes

AF:

0.773

AC:

117461

AN:

151908

Hom.:

45617

Cov.:

show subpopulations

Gnomad AFR

AF:

0.727

Gnomad AMI

AF:

0.899

Gnomad AMR

AF:

0.841

Gnomad ASJ

AF:

0.888

Gnomad EAS

AF:

0.846

Gnomad SAS

AF:

0.931

Gnomad FIN

AF:

0.707

Gnomad MID

AF:

0.896

Gnomad NFE

AF:

0.770

Gnomad OTH

AF:

0.813

GnomAD4 exome

AF:

1.00

AC:

AN:

Hom.:

Cov.:

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

1.00

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AC:

AN:

Other (OTH)

AC:

AN:

Age Distribution

Exome Hom

Variant carriers

<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:

0.773

AC:

117557

AN:

152026

Hom.:

45658

Cov.:

AF XY:

0.776

AC XY:

57711

AN XY:

74322

show subpopulations

African (AFR)

AF:

0.727

AC:

30119

AN:

41410

American (AMR)

AF:

0.841

AC:

12857

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.888

AC:

3080

AN:

3470

East Asian (EAS)

AF:

0.846

AC:

4366

AN:

5162

South Asian (SAS)

AF:

0.931

AC:

4487

AN:

4818

European-Finnish (FIN)

AF:

0.707

AC:

7472

AN:

10568

Middle Eastern (MID)

AF:

0.895

AC:

263

AN:

294

European-Non Finnish (NFE)

AF:

0.770

AC:

52373

AN:

68004

Other (OTH)

AF:

0.816

AC:

1720

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

1349

2698

4046

5395

6744

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

868

1736

2604

3472

4340

<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:

0.771

Hom.:

5978

Bravo

AF:

0.778

Asia WGS

AF:

0.887

AC:

3086

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

6.1

(source)

DANN

Benign

0.37

PhyloP100

2.3

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