11-125593855-GTGT-G

Position:

• chr11-125593855-GTGT-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_152713.5(STT3A):​c.-36+948_-36+950del variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.46 (17213 hom., cov: 0)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: STT3A NM_152713.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.906

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]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 11-125593855-GTGT-G is Benign according to our data. Variant chr11-125593855-GTGT-G is described in ClinVar as [Benign]. Clinvar id is 1292244.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.58 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
STT3A	NM_152713.5	c.-36+948_-36+950del		intron_variant		ENST00000392708.9	NP_689926.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
STT3A	ENST00000392708.9	c.-36+948_-36+950del		intron_variant		1	NM_152713.5	ENSP00000376472	P1

Frequencies

GnomAD3 genomes AF: 0.458 AC: 69441 AN: 151560 Hom.: 17207 Cov.: 0

Gnomad AFR AF: 0.243

Gnomad AMI AF: 0.465

Gnomad AMR AF: 0.572

Gnomad ASJ AF: 0.525

Gnomad EAS AF: 0.517

Gnomad SAS AF: 0.597

Gnomad FIN AF: 0.438

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.548

Gnomad OTH AF: 0.474

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 2 Hom.: 0 AC XY: 0 AN XY: 0

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.458 AC: 69456 AN: 151678 Hom.: 17213 Cov.: 0 AF XY: 0.457 AC XY: 33884 AN XY: 74092

Gnomad4 AFR AF: 0.243

Gnomad4 AMR AF: 0.572

Gnomad4 ASJ AF: 0.525

Gnomad4 EAS AF: 0.517

Gnomad4 SAS AF: 0.598

Gnomad4 FIN AF: 0.438

Gnomad4 NFE AF: 0.548

Gnomad4 OTH AF: 0.476

Bravo AF: 0.457

Asia WGS AF: 0.523 AC: 1820 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 29, 2018

- -

Computational scores

Source: dbNSFP v4.3

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

Other links and lift over

dbSNP: rs10538228; hg19: chr11-125463750;