11-125596106-A-G

Position:

• chr11-125596106-A-G

Variant summary

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

The NM_152713.5(STT3A):​c.88+103A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0651 in 890,458 control chromosomes in the GnomAD database, including 2,774 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.11 (1219 hom., cov: 32)
  • Exomes 𝑓: 0.057 (1555 hom.)
• Consequence: STT3A NM_152713.5 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.271

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=-0.83).
• BP6: Variant 11-125596106-A-G is Benign according to our data. Variant chr11-125596106-A-G is described in ClinVar as [Benign]. Clinvar id is 1292105.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.215 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
STT3A	NM_152713.5	c.88+103A>G		intron_variant		ENST00000392708.9	NP_689926.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
STT3A	ENST00000392708.9	c.88+103A>G		intron_variant		1	NM_152713.5	ENSP00000376472	P1

Frequencies

GnomAD3 genomes AF: 0.106 AC: 16172 AN: 152054 Hom.: 1215 Cov.: 32

Gnomad AFR AF: 0.218

Gnomad AMI AF: 0.233

Gnomad AMR AF: 0.0648

Gnomad ASJ AF: 0.0784

Gnomad EAS AF: 0.0215

Gnomad SAS AF: 0.0553

Gnomad FIN AF: 0.0437

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0673

Gnomad OTH AF: 0.108

GnomAD4 exome AF: 0.0566 AC: 41752 AN: 738286 Hom.: 1555 AF XY: 0.0557 AC XY: 21531 AN XY: 386350

Gnomad4 AFR exome AF: 0.206

Gnomad4 AMR exome AF: 0.0466

Gnomad4 ASJ exome AF: 0.0732

Gnomad4 EAS exome AF: 0.0172

Gnomad4 SAS exome AF: 0.0438

Gnomad4 FIN exome AF: 0.0476

Gnomad4 NFE exome AF: 0.0551

Gnomad4 OTH exome AF: 0.0711

GnomAD4 genome AF: 0.106 AC: 16202 AN: 152172 Hom.: 1219 Cov.: 32 AF XY: 0.103 AC XY: 7693 AN XY: 74426

Gnomad4 AFR AF: 0.218

Gnomad4 AMR AF: 0.0648

Gnomad4 ASJ AF: 0.0784

Gnomad4 EAS AF: 0.0218

Gnomad4 SAS AF: 0.0551

Gnomad4 FIN AF: 0.0437

Gnomad4 NFE AF: 0.0673

Gnomad4 OTH AF: 0.106

Alfa AF: 0.0849 Hom.: 91

Bravo AF: 0.114

Asia WGS AF: 0.0600 AC: 207 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	clinical testing	GeneDx	Sep 07, 2018	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	8.6
DANN	Benign	0.80
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs12289190; hg19: chr11-125466001;