11-125596781-G-T

Position:

• chr11-125596781-G-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_152713.5(STT3A):​c.89-278G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.077 in 152,176 control chromosomes in the GnomAD database, including 516 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.077 (516 hom., cov: 32)
• Consequence: STT3A NM_152713.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.304

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 -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.62).
• BP6: Variant 11-125596781-G-T is Benign according to our data. Variant chr11-125596781-G-T is described in ClinVar as [Benign]. Clinvar id is 1244349.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.117 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
STT3A	NM_152713.5	c.89-278G>T		intron_variant		ENST00000392708.9	NP_689926.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
STT3A	ENST00000392708.9	c.89-278G>T		intron_variant		1	NM_152713.5	ENSP00000376472	P1

Frequencies

GnomAD3 genomes AF: 0.0770 AC: 11701 AN: 152058 Hom.: 515 Cov.: 32

Gnomad AFR AF: 0.120

Gnomad AMI AF: 0.232

Gnomad AMR AF: 0.0517

Gnomad ASJ AF: 0.0779

Gnomad EAS AF: 0.00212

Gnomad SAS AF: 0.0508

Gnomad FIN AF: 0.0436

Gnomad MID AF: 0.102

Gnomad NFE AF: 0.0668

Gnomad OTH AF: 0.0880

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0770 AC: 11717 AN: 152176 Hom.: 516 Cov.: 32 AF XY: 0.0747 AC XY: 5556 AN XY: 74408

Gnomad4 AFR AF: 0.120

Gnomad4 AMR AF: 0.0517

Gnomad4 ASJ AF: 0.0779

Gnomad4 EAS AF: 0.00212

Gnomad4 SAS AF: 0.0510

Gnomad4 FIN AF: 0.0436

Gnomad4 NFE AF: 0.0667

Gnomad4 OTH AF: 0.0861

Alfa AF: 0.0286 Hom.: 18

Bravo AF: 0.0798

Asia WGS AF: 0.0370 AC: 128 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

Sep 07, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	13
DANN	Benign	0.82

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: rs78574330; hg19: chr11-125466676;