Variant 12-22201987-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_003034.4(ST8SIA1):c.636T>C(p.Ile212=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.779 in 1,613,074 control chromosomes in the GnomAD database, including 491,362 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 ( 45808 hom., cov: 31)

Exomes 𝑓: 0.78 ( 445554 hom. )

Consequence

ST8SIA1
NM_003034.4 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.375

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 made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.51).

BP7

Synonymous conserved (PhyloP=0.375 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.908 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ST8SIA1	NM_003034.4 linkuse as main transcript	c.636T>C	p.Ile212=	synonymous_variant	5/5	ENST00000396037.9	NP_003025.1
ST8SIA1	NM_001304450.2 linkuse as main transcript	c.207T>C	p.Ile69=	synonymous_variant	4/4		NP_001291379.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ST8SIA1	ENST00000396037.9 linkuse as main transcript	c.636T>C	p.Ile212=	synonymous_variant	5/5	1	NM_003034.4	ENSP00000379353	P1	Q92185-1

Frequencies

GnomAD3 genomes

AF:

0.774

AC:

117648

AN:

151902

Hom.:

45767

Cov.:

show subpopulations

Gnomad AFR

AF:

0.730

Gnomad AMI

AF:

0.899

Gnomad AMR

AF:

0.842

Gnomad ASJ

AF:

0.887

Gnomad EAS

AF:

0.847

Gnomad SAS

AF:

0.931

Gnomad FIN

AF:

0.706

Gnomad MID

AF:

0.899

Gnomad NFE

AF:

0.771

Gnomad OTH

AF:

0.814

GnomAD3 exomes

AF:

0.808

AC:

200388

AN:

247918

Hom.:

81766

AF XY:

0.814

AC XY:

109302

AN XY:

134224

show subpopulations

Gnomad AFR exome

AF:

0.725

Gnomad AMR exome

AF:

0.858

Gnomad ASJ exome

AF:

0.880

Gnomad EAS exome

AF:

0.844

Gnomad SAS exome

AF:

0.933

Gnomad FIN exome

AF:

0.716

Gnomad NFE exome

AF:

0.776

Gnomad OTH exome

AF:

0.814

GnomAD4 exome

AF:

0.779

AC:

1138146

AN:

1461054

Hom.:

445554

Cov.:

AF XY:

0.784

AC XY:

570100

AN XY:

726816

show subpopulations

Gnomad4 AFR exome

AF:

0.723

Gnomad4 AMR exome

AF:

0.857

Gnomad4 ASJ exome

AF:

0.880

Gnomad4 EAS exome

AF:

0.861

Gnomad4 SAS exome

AF:

0.930

Gnomad4 FIN exome

AF:

0.722

Gnomad4 NFE exome

AF:

0.762

Gnomad4 OTH exome

AF:

0.793

GnomAD4 genome

AF:

0.775

AC:

117744

AN:

152020

Hom.:

45808

Cov.:

AF XY:

0.778

AC XY:

57776

AN XY:

74308

show subpopulations

Gnomad4 AFR

AF:

0.730

Gnomad4 AMR

AF:

0.843

Gnomad4 ASJ

AF:

0.887

Gnomad4 EAS

AF:

0.846

Gnomad4 SAS

AF:

0.931

Gnomad4 FIN

AF:

0.706

Gnomad4 NFE

AF:

0.771

Gnomad4 OTH

AF:

0.817

Alfa

AF:

0.785

Hom.:

93406

Bravo

AF:

0.780

Asia WGS

AF:

0.888

AC:

3089

AN:

3478

EpiCase

AF:

0.789

EpiControl

AF:

0.789

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.51

CADD

Benign

5.8

DANN

Benign

0.77

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over