Variant rs1048479 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_173344.3(ST3GAL1):c.819G>A(p.Ser273Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.495 in 1,613,692 control chromosomes in the GnomAD database, including 200,098 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 0.47 ( 17362 hom., cov: 31)

Exomes 𝑓: 0.50 ( 182736 hom. )

Consequence

ST3GAL1
NM_173344.3 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.07

Variant links:

Genes affected

ST3GAL1 (HGNC:10862): (ST3 beta-galactoside alpha-2,3-sialyltransferase 1) The protein encoded by this gene is a type II membrane protein that catalyzes the transfer of sialic acid from CMP-sialic acid to galactose-containing substrates. The encoded protein is normally found in the Golgi but can be proteolytically processed to a soluble form. Correct glycosylation of the encoded protein may be critical to its sialyltransferase activity. This protein, which is a member of glycosyltransferase family 29, can use the same acceptor substrates as does sialyltransferase 4B. Two transcript variants encoding the same protein have been found for this gene. Other transcript variants may exist, but have not been fully characterized yet. [provided by RefSeq, Jul 2008]

ST3GAL1 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=-0.55).

BP7

Synonymous conserved (PhyloP=-3.07 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.607 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ST3GAL1	NM_173344.3 linkuse as main transcript	c.819G>A	p.Ser273Ser	synonymous_variant	9/10	ENST00000522652.6	NP_775479.1	Q11201A0A024R9L6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
ST3GAL1	ENST00000522652.6 linkuse as main transcript	c.819G>A	p.Ser273Ser	synonymous_variant	9/10	1	NM_173344.3	ENSP00000430515.1	Q11201
ST3GAL1	ENST00000521180.5 linkuse as main transcript	c.819G>A	p.Ser273Ser	synonymous_variant	8/9	1		ENSP00000428540.1	Q11201
ST3GAL1	ENST00000648219.1 linkuse as main transcript	c.819G>A	p.Ser273Ser	synonymous_variant	11/12			ENSP00000497381.1	Q11201

Frequencies

GnomAD3 genomes

AF:

0.472

AC:

71730

AN:

151832

Hom.:

17360

Cov.:

show subpopulations

Gnomad AFR

AF:

0.374

Gnomad AMI

AF:

0.476

Gnomad AMR

AF:

0.618

Gnomad ASJ

AF:

0.399

Gnomad EAS

AF:

0.454

Gnomad SAS

AF:

0.523

Gnomad FIN

AF:

0.526

Gnomad MID

AF:

0.566

Gnomad NFE

AF:

0.491

Gnomad OTH

AF:

0.522

GnomAD3 exomes

AF:

0.509

AC:

127874

AN:

251402

Hom.:

33585

AF XY:

0.507

AC XY:

68947

AN XY:

135868

show subpopulations

Gnomad AFR exome

AF:

0.371

Gnomad AMR exome

AF:

0.675

Gnomad ASJ exome

AF:

0.394

Gnomad EAS exome

AF:

0.452

Gnomad SAS exome

AF:

0.526

Gnomad FIN exome

AF:

0.517

Gnomad NFE exome

AF:

0.490

Gnomad OTH exome

AF:

0.523

GnomAD4 exome

AF:

0.497

AC:

727053

AN:

1461742

Hom.:

182736

Cov.:

AF XY:

0.497

AC XY:

361734

AN XY:

727182

show subpopulations

Gnomad4 AFR exome

AF:

0.375

Gnomad4 AMR exome

AF:

0.670

Gnomad4 ASJ exome

AF:

0.398

Gnomad4 EAS exome

AF:

0.416

Gnomad4 SAS exome

AF:

0.531

Gnomad4 FIN exome

AF:

0.518

Gnomad4 NFE exome

AF:

0.496

Gnomad4 OTH exome

AF:

0.497

GnomAD4 genome

AF:

0.472

AC:

71749

AN:

151950

Hom.:

17362

Cov.:

AF XY:

0.479

AC XY:

35588

AN XY:

74272

show subpopulations

Gnomad4 AFR

AF:

0.374

Gnomad4 AMR

AF:

0.617

Gnomad4 ASJ

AF:

0.399

Gnomad4 EAS

AF:

0.454

Gnomad4 SAS

AF:

0.524

Gnomad4 FIN

AF:

0.526

Gnomad4 NFE

AF:

0.491

Gnomad4 OTH

AF:

0.518

Alfa

AF:

0.471

Hom.:

7874

Bravo

AF:

0.476

Asia WGS

AF:

0.484

AC:

1685

AN:

3478

EpiCase

AF:

0.499

EpiControl

AF:

0.494

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.55

CADD

Benign

0.027

DANN

Benign

0.65

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