rs10082632

Variant names:

Variant summary

Our verdict is Benign. The variant received -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_152713.5(STT3A):c.52T>C(p.Leu18Leu) 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

Publications

17 publications found

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 Gene-Disease associations (from GenCC):

congenital disorder of glycosylation, type Iw, autosomal dominant
Inheritance: AD Classification: STRONG, MODERATE Submitted by: G2P, Ambry Genetics, Labcorp Genetics (formerly Invitae)
STT3A-congenital disorder of glycosylation
Inheritance: AR Classification: STRONG, MODERATE, SUPPORTIVE, LIMITED Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae), Orphanet, G2P

STT3A links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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 VariationId 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 rank	MANE	Protein	UniProt
STT3A	NM_152713.5 link	c.52T>C	p.Leu18Leu	synonymous_variant	Exon 2 of 18	ENST00000392708.9	NP_689926.1	P46977-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STT3A	ENST00000392708.9 link	c.52T>C	p.Leu18Leu	synonymous_variant	Exon 2 of 18	1	NM_152713.5	ENSP00000376472.3		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

GnomAD2 exomes

AF:

0.0689

AC:

17304

AN:

251086

AF XY:

0.0660

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 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

African (AFR)

AF:

0.233

AC:

7764

AN:

33368

American (AMR)

AF:

0.0472

AC:

2108

AN:

44694

Ashkenazi Jewish (ASJ)

AF:

0.0786

AC:

2054

AN:

26126

East Asian (EAS)

AF:

0.0189

AC:

749

AN:

39688

South Asian (SAS)

AF:

0.0483

AC:

4162

AN:

86180

European-Finnish (FIN)

AF:

0.0486

AC:

2597

AN:

53408

Middle Eastern (MID)

AF:

0.117

AC:

674

AN:

5764

European-Non Finnish (NFE)

AF:

0.0671

AC:

74542

AN:

1110502

Other (OTH)

AF:

0.0775

AC:

4677

AN:

60336

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.430

Heterozygous variant carriers

4529

9059

13588

18118

22647

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

2852

5704

8556

11408

14260

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.107

AC:

16270

AN:

152274

Hom.:

1256

Cov.:

AF XY:

0.104

AC XY:

7717

AN XY:

74452

show subpopulations

African (AFR)

AF:

0.220

AC:

9127

AN:

41544

American (AMR)

AF:

0.0647

AC:

989

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.0784

AC:

272

AN:

3470

East Asian (EAS)

AF:

0.0219

AC:

114

AN:

5194

South Asian (SAS)

AF:

0.0545

AC:

263

AN:

4822

European-Finnish (FIN)

AF:

0.0437

AC:

463

AN:

10604

Middle Eastern (MID)

AF:

0.0986

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0673

AC:

4576

AN:

68030

Other (OTH)

AF:

0.106

AC:

223

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

712

1424

2136

2848

3560

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

168

336

504

672

840

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0911

Hom.:

392

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

Breakthrough Genomics, Breakthrough Genomics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:not provided

- -

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

not specified

Benign:1

Dec 21, 2015

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

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

(source)

DANN

Benign

0.84

PhyloP100

2.6

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over