Variant chr11-125595967-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_152713.5(STT3A):c.52T>C(p.Leu18=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0717 in 1,612,340 control chromosomes in the GnomAD database, including 5,358 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.11 ( 1256 hom., cov: 33)

Exomes 𝑓: 0.068 ( 4102 hom. )

Consequence

STT3A
NM_152713.5 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 2.58

Variant links:

Genes affected

STT3A (HGNC:6172): (STT3 oligosaccharyltransferase complex catalytic subunit A) The protein encoded by this gene is a catalytic subunit of the N-oligosaccharyltransferase (OST) complex, which functions in the endoplasmic reticulum to transfer glycan chains to asparagine residues of target proteins. A separate complex containing a similar catalytic subunit with an overlapping function also exists. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2015]

STT3A 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=-0.54).

BP6

Variant 11-125595967-T-C is Benign according to our data. Variant chr11-125595967-T-C is described in ClinVar as [Benign]. Clinvar id is 380012.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=2.58 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.216 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
STT3A	NM_152713.5 linkuse as main transcript	c.52T>C	p.Leu18=	synonymous_variant	2/18	ENST00000392708.9	NP_689926.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
STT3A	ENST00000392708.9 linkuse as main transcript	c.52T>C	p.Leu18=	synonymous_variant	2/18	1	NM_152713.5	ENSP00000376472	P1	P46977-1

Frequencies

GnomAD3 genomes

AF:

0.107

AC:

16239

AN:

152156

Hom.:

1252

Cov.:

show subpopulations

Gnomad AFR

AF:

0.219

Gnomad AMI

AF:

0.235

Gnomad AMR

AF:

0.0648

Gnomad ASJ

AF:

0.0784

Gnomad EAS

AF:

0.0217

Gnomad SAS

AF:

0.0547

Gnomad FIN

AF:

0.0437

Gnomad MID

AF:

0.101

Gnomad NFE

AF:

0.0673

Gnomad OTH

AF:

0.108

GnomAD3 exomes

AF:

0.0689

AC:

17304

AN:

251086

Hom.:

841

AF XY:

0.0660

AC XY:

8956

AN XY:

135714

show subpopulations

Gnomad AFR exome

AF:

0.223

Gnomad AMR exome

AF:

0.0435

Gnomad ASJ exome

AF:

0.0794

Gnomad EAS exome

AF:

0.0243

Gnomad SAS exome

AF:

0.0484

Gnomad FIN exome

AF:

0.0459

Gnomad NFE exome

AF:

0.0702

Gnomad OTH exome

AF:

0.0815

GnomAD4 exome

AF:

0.0680

AC:

99327

AN:

1460066

Hom.:

4102

Cov.:

AF XY:

0.0666

AC XY:

48362

AN XY:

726394

show subpopulations

Gnomad4 AFR exome

AF:

0.233

Gnomad4 AMR exome

AF:

0.0472

Gnomad4 ASJ exome

AF:

0.0786

Gnomad4 EAS exome

AF:

0.0189

Gnomad4 SAS exome

AF:

0.0483

Gnomad4 FIN exome

AF:

0.0486

Gnomad4 NFE exome

AF:

0.0671

Gnomad4 OTH exome

AF:

0.0775

GnomAD4 genome

AF:

0.107

AC:

16270

AN:

152274

Hom.:

1256

Cov.:

AF XY:

0.104

AC XY:

7717

AN XY:

74452

show subpopulations

Gnomad4 AFR

AF:

0.220

Gnomad4 AMR

AF:

0.0647

Gnomad4 ASJ

AF:

0.0784

Gnomad4 EAS

AF:

0.0219

Gnomad4 SAS

AF:

0.0545

Gnomad4 FIN

AF:

0.0437

Gnomad4 NFE

AF:

0.0673

Gnomad4 OTH

AF:

0.106

Alfa

AF:

0.0898

Hom.:

378

Bravo

AF:

0.114

Asia WGS

AF:

0.0610

AC:

211

AN:

3478

EpiCase

AF:

0.0712

EpiControl

AF:

0.0720

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 29, 2024	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Dec 21, 2015

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.54

CADD

Benign

8.1

DANN

Benign

0.84

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

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