Variant 11-126408308-T-C 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.439T>C(p.Leu147=) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0787 in 1,613,794 control chromosomes in the GnomAD database, including 5,939 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.073 ( 577 hom., cov: 32)

Exomes 𝑓: 0.079 ( 5362 hom. )

Consequence

ST3GAL4
NM_001254757.2 splice_region, synonymous

Scores

Splicing: ADA: 0.0002615

Clinical Significance

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

Conservation

PhyloP100: -0.657

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.65).

BP6

Variant 11-126408308-T-C is Benign according to our data. Variant chr11-126408308-T-C is described in ClinVar as [Benign]. Clinvar id is 257675.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.657 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.195 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.439T>C	p.Leu147=	splice_region_variant, synonymous_variant	8/11	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.439T>C	p.Leu147=	splice_region_variant, synonymous_variant	8/11	5	NM_001254757.2	ENSP00000394354	P4	Q11206-1

Frequencies

GnomAD3 genomes

AF:

0.0726

AC:

11040

AN:

152042

Hom.:

575

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0224

Gnomad AMI

AF:

0.0570

Gnomad AMR

AF:

0.112

Gnomad ASJ

AF:

0.0392

Gnomad EAS

AF:

0.205

Gnomad SAS

AF:

0.0608

Gnomad FIN

AF:

0.111

Gnomad MID

AF:

0.0285

Gnomad NFE

AF:

0.0810

Gnomad OTH

AF:

0.0761

GnomAD3 exomes

AF:

0.0865

AC:

21748

AN:

251306

Hom.:

1170

AF XY:

0.0841

AC XY:

11419

AN XY:

135830

show subpopulations

Gnomad AFR exome

AF:

0.0200

Gnomad AMR exome

AF:

0.0993

Gnomad ASJ exome

AF:

0.0425

Gnomad EAS exome

AF:

0.211

Gnomad SAS exome

AF:

0.0571

Gnomad FIN exome

AF:

0.105

Gnomad NFE exome

AF:

0.0805

Gnomad OTH exome

AF:

0.0814

GnomAD4 exome

AF:

0.0793

AC:

115884

AN:

1461634

Hom.:

5362

Cov.:

AF XY:

0.0785

AC XY:

57092

AN XY:

727070

show subpopulations

Gnomad4 AFR exome

AF:

0.0183

Gnomad4 AMR exome

AF:

0.0970

Gnomad4 ASJ exome

AF:

0.0432

Gnomad4 EAS exome

AF:

0.220

Gnomad4 SAS exome

AF:

0.0575

Gnomad4 FIN exome

AF:

0.104

Gnomad4 NFE exome

AF:

0.0772

Gnomad4 OTH exome

AF:

0.0734

GnomAD4 genome

AF:

0.0726

AC:

11043

AN:

152160

Hom.:

577

Cov.:

AF XY:

0.0773

AC XY:

5748

AN XY:

74400

show subpopulations

Gnomad4 AFR

AF:

0.0223

Gnomad4 AMR

AF:

0.113

Gnomad4 ASJ

AF:

0.0392

Gnomad4 EAS

AF:

0.205

Gnomad4 SAS

AF:

0.0610

Gnomad4 FIN

AF:

0.111

Gnomad4 NFE

AF:

0.0810

Gnomad4 OTH

AF:

0.0767

Alfa

AF:

0.0770

Hom.:

1279

Bravo

AF:

0.0698

Asia WGS

AF:

0.122

AC:

422

AN:

3478

EpiCase

AF:

0.0736

EpiControl

AF:

0.0734

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

-0.65

CADD

Benign

0.53

DANN

Benign

0.49

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.00026

dbscSNV1_RF

Benign

0.040

SpliceAI score (max)

0.010

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