Variant rs2230279 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_001254757.2(ST3GAL4):c.423C>T(p.Tyr141Tyr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.309 in 1,613,724 control chromosomes in the GnomAD database, including 78,523 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.32 ( 7782 hom., cov: 32)

Exomes 𝑓: 0.31 ( 70741 hom. )

Consequence

ST3GAL4
NM_001254757.2 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.932

Variant links:

Genes affected

ST3GAL4 (HGNC:10864): (ST3 beta-galactoside alpha-2,3-sialyltransferase 4) This gene encodes a member of the glycosyltransferase 29 family, a group of enzymes involved in protein glycosylation. The encoded protein is targeted to Golgi membranes but may be proteolytically processed and secreted. The gene product may also be involved in the increased expression of sialyl Lewis X antigen seen in inflammatory responses. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2011]

ST3GAL4 links:

ST3GAL4 (HGNC:):

ST3GAL4 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.5).

BP6

Variant 11-126408180-C-T is Benign according to our data. Variant chr11-126408180-C-T is described in ClinVar as [Benign]. Clinvar id is 257674.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.932 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.499 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ST3GAL4	NM_001254757.2 linkuse as main transcript	c.423C>T	p.Tyr141Tyr	synonymous_variant	7/11	ENST00000444328.7	NP_001241686.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ST3GAL4	ENST00000444328.7 linkuse as main transcript	c.423C>T	p.Tyr141Tyr	synonymous_variant	7/11	5	NM_001254757.2	ENSP00000394354.2		Q11206-1

Frequencies

GnomAD3 genomes

AF:

0.315

AC:

47892

AN:

151904

Hom.:

7779

Cov.:

show subpopulations

Gnomad AFR

AF:

0.345

Gnomad AMI

AF:

0.290

Gnomad AMR

AF:

0.322

Gnomad ASJ

AF:

0.364

Gnomad EAS

AF:

0.515

Gnomad SAS

AF:

0.231

Gnomad FIN

AF:

0.221

Gnomad MID

AF:

0.278

Gnomad NFE

AF:

0.299

Gnomad OTH

AF:

0.324

GnomAD3 exomes

AF:

0.314

AC:

78937

AN:

251328

Hom.:

13122

AF XY:

0.308

AC XY:

41825

AN XY:

135838

show subpopulations

Gnomad AFR exome

AF:

0.353

Gnomad AMR exome

AF:

0.340

Gnomad ASJ exome

AF:

0.362

Gnomad EAS exome

AF:

0.512

Gnomad SAS exome

AF:

0.226

Gnomad FIN exome

AF:

0.220

Gnomad NFE exome

AF:

0.306

Gnomad OTH exome

AF:

0.317

GnomAD4 exome

AF:

0.308

AC:

450462

AN:

1461702

Hom.:

70741

Cov.:

AF XY:

0.305

AC XY:

222088

AN XY:

727138

show subpopulations

Gnomad4 AFR exome

AF:

0.358

Gnomad4 AMR exome

AF:

0.332

Gnomad4 ASJ exome

AF:

0.363

Gnomad4 EAS exome

AF:

0.469

Gnomad4 SAS exome

AF:

0.233

Gnomad4 FIN exome

AF:

0.229

Gnomad4 NFE exome

AF:

0.308

Gnomad4 OTH exome

AF:

0.314

GnomAD4 genome

AF:

0.315

AC:

47924

AN:

152022

Hom.:

7782

Cov.:

AF XY:

0.311

AC XY:

23139

AN XY:

74284

show subpopulations

Gnomad4 AFR

AF:

0.345

Gnomad4 AMR

AF:

0.322

Gnomad4 ASJ

AF:

0.364

Gnomad4 EAS

AF:

0.515

Gnomad4 SAS

AF:

0.231

Gnomad4 FIN

AF:

0.221

Gnomad4 NFE

AF:

0.299

Gnomad4 OTH

AF:

0.321

Alfa

AF:

0.309

Hom.:

17287

Bravo

AF:

0.329

Asia WGS

AF:

0.328

AC:

1140

AN:

3478

EpiCase

AF:

0.309

EpiControl

AF:

0.304

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

not provided

Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.50

CADD

Benign

3.1

DANN

Benign

0.72

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over