11-125592747-G-A

Position:

• chr11-125592747-G-A

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The ENST00000527606.5(STT3A):​c.-36+860G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0751 in 291,638 control chromosomes in the GnomAD database, including 1,014 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.085 (622 hom., cov: 32)
  • Exomes 𝑓: 0.064 (392 hom.)
• Consequence: STT3A ENST00000527606.5 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.669

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 -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BP6: Variant 11-125592747-G-A is Benign according to our data. Variant chr11-125592747-G-A is described in ClinVar as [Benign]. Clinvar id is 1275875.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.119 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
STT3A	XM_047426897.1	c.-252+860G>A		intron_variant			XP_047282853.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
STT3A	ENST00000527606.5	c.-36+860G>A		intron_variant		4		ENSP00000436558

Frequencies

GnomAD3 genomes AF: 0.0849 AC: 12912 AN: 152050 Hom.: 621 Cov.: 32

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.235

Gnomad AMR AF: 0.0643

Gnomad ASJ AF: 0.0911

Gnomad EAS AF: 0.00212

Gnomad SAS AF: 0.0427

Gnomad FIN AF: 0.0502

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0792

Gnomad OTH AF: 0.0925

GnomAD4 exome AF: 0.0643 AC: 8967 AN: 139470 Hom.: 392 Cov.: 0 AF XY: 0.0612 AC XY: 4779 AN XY: 78040

Gnomad4 AFR exome AF: 0.122

Gnomad4 AMR exome AF: 0.0431

Gnomad4 ASJ exome AF: 0.0802

Gnomad4 EAS exome AF: 0.000600

Gnomad4 SAS exome AF: 0.0409

Gnomad4 FIN exome AF: 0.0567

Gnomad4 NFE exome AF: 0.0765

Gnomad4 OTH exome AF: 0.0779

GnomAD4 genome AF: 0.0850 AC: 12930 AN: 152168 Hom.: 622 Cov.: 32 AF XY: 0.0824 AC XY: 6129 AN XY: 74410

Gnomad4 AFR AF: 0.122

Gnomad4 AMR AF: 0.0642

Gnomad4 ASJ AF: 0.0911

Gnomad4 EAS AF: 0.00213

Gnomad4 SAS AF: 0.0431

Gnomad4 FIN AF: 0.0502

Gnomad4 NFE AF: 0.0792

Gnomad4 OTH AF: 0.0911

Alfa AF: 0.0815 Hom.: 154

Bravo AF: 0.0879

Asia WGS AF: 0.0370 AC: 127 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 29, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	1.8
DANN	Benign	0.70

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs11220141; hg19: chr11-125462642;