Variant chr11-125596010-G-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_152713.5(STT3A):c.88+7G>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0621 in 1,595,324 control chromosomes in the GnomAD database, including 3,474 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 0.070 ( 409 hom., cov: 32)

Exomes 𝑓: 0.061 ( 3065 hom. )

Consequence

STT3A
NM_152713.5 splice_region, intron

Scores

Splicing: ADA: 0.0001904

Clinical Significance

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

Conservation

PhyloP100: -0.0150

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 -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.86).

BP6

Variant 11-125596010-G-T is Benign according to our data. Variant chr11-125596010-G-T is described in ClinVar as [Benign]. Clinvar id is 380013.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0948 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.88+7G>T		splice_region_variant, intron_variant		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.88+7G>T		splice_region_variant, intron_variant		1	NM_152713.5	ENSP00000376472	P1	P46977-1

Frequencies

GnomAD3 genomes

AF:

0.0702

AC:

10680

AN:

152132

Hom.:

408

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0972

Gnomad AMI

AF:

0.235

Gnomad AMR

AF:

0.0495

Gnomad ASJ

AF:

0.0778

Gnomad EAS

AF:

0.00211

Gnomad SAS

AF:

0.0404

Gnomad FIN

AF:

0.0437

Gnomad MID

AF:

0.101

Gnomad NFE

AF:

0.0668

Gnomad OTH

AF:

0.0832

GnomAD3 exomes

AF:

0.0560

AC:

13691

AN:

244632

Hom.:

467

AF XY:

0.0554

AC XY:

7316

AN XY:

132122

show subpopulations

Gnomad AFR exome

AF:

0.0978

Gnomad AMR exome

AF:

0.0361

Gnomad ASJ exome

AF:

0.0756

Gnomad EAS exome

AF:

0.000664

Gnomad SAS exome

AF:

0.0384

Gnomad FIN exome

AF:

0.0458

Gnomad NFE exome

AF:

0.0687

Gnomad OTH exome

AF:

0.0701

GnomAD4 exome

AF:

0.0612

AC:

88317

AN:

1443074

Hom.:

3065

Cov.:

AF XY:

0.0602

AC XY:

43243

AN XY:

718328

show subpopulations

Gnomad4 AFR exome

AF:

0.101

Gnomad4 AMR exome

AF:

0.0387

Gnomad4 ASJ exome

AF:

0.0751

Gnomad4 EAS exome

AF:

0.000457

Gnomad4 SAS exome

AF:

0.0379

Gnomad4 FIN exome

AF:

0.0484

Gnomad4 NFE exome

AF:

0.0647

Gnomad4 OTH exome

AF:

0.0654

GnomAD4 genome

AF:

0.0702

AC:

10692

AN:

152250

Hom.:

409

Cov.:

AF XY:

0.0680

AC XY:

5063

AN XY:

74452

show subpopulations

Gnomad4 AFR

AF:

0.0973

Gnomad4 AMR

AF:

0.0495

Gnomad4 ASJ

AF:

0.0778

Gnomad4 EAS

AF:

0.00212

Gnomad4 SAS

AF:

0.0409

Gnomad4 FIN

AF:

0.0437

Gnomad4 NFE

AF:

0.0667

Gnomad4 OTH

AF:

0.0818

Alfa

AF:

0.0718

Hom.:

166

Bravo

AF:

0.0727

Asia WGS

AF:

0.0330

AC:

113

AN:

3478

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

-0.86

CADD

Benign

8.3

DANN

Benign

0.74

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.00019

dbscSNV1_RF

Benign

0.012

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