Variant 11-125591814-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000527606(STT3A):c.-109A>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.833 in 152,326 control chromosomes in the GnomAD database, including 53,295 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.83 ( 53210 hom., cov: 31)

Exomes 𝑓: 0.92 ( 85 hom. )

Consequence

STT3A
ENST00000527606 5_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.70

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:

FEZ1 (HGNC:3659): (fasciculation and elongation protein zeta 1) This gene is an ortholog of the C. elegans unc-76 gene, which is necessary for normal axonal bundling and elongation within axon bundles. Expression of this gene in C. elegans unc-76 mutants can restore to the mutants partial locomotion and axonal fasciculation, suggesting that it also functions in axonal outgrowth. The N-terminal half of the gene product is highly acidic. Alternatively spliced transcript variants encoding different isoforms of this protein have been described. [provided by RefSeq, Jul 2008]

FEZ1 links:

STT3A-AS1 (HGNC:44585): (STT3A antisense RNA 1)

STT3A-AS1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.919 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
STT3A	XM_047426897.1 link	c.-325A>G		5_prime_UTR_variant	1/19		XP_047282853.1
STT3A-AS1	NR_132372.1 link	n.151+604T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	Protein	UniProt
STT3A	ENST00000527606 link	c.-109A>G	5_prime_UTR_variant	1/5	4	ENSP00000436558.1	E9PI32
FEZ1	ENST00000648911.1 link	c.-259+604T>C	intron_variant			ENSP00000497070.1	Q99689-1
FEZ1	ENST00000530526.1 link	n.151+604T>C	intron_variant		3

Frequencies

GnomAD3 genomes

AF:

0.833

AC:

126614

AN:

152006

Hom.:

53175

Cov.:

show subpopulations

Gnomad AFR

AF:

0.714

Gnomad AMI

AF:

0.885

Gnomad AMR

AF:

0.858

Gnomad ASJ

AF:

0.879

Gnomad EAS

AF:

0.884

Gnomad SAS

AF:

0.941

Gnomad FIN

AF:

0.815

Gnomad MID

AF:

0.889

Gnomad NFE

AF:

0.887

Gnomad OTH

AF:

0.854

GnomAD4 exome

AF:

0.916

AC:

185

AN:

202

Hom.:

Cov.:

AF XY:

0.934

AC XY:

114

AN XY:

122

show subpopulations

Gnomad4 AFR exome

AF:

0.667

Gnomad4 AMR exome

AF:

1.00

Gnomad4 ASJ exome

AF:

1.00

Gnomad4 EAS exome

AF:

0.833

Gnomad4 SAS exome

AF:

1.00

Gnomad4 FIN exome

AF:

1.00

Gnomad4 NFE exome

AF:

0.881

Gnomad4 OTH exome

AF:

1.00

GnomAD4 genome

AF:

0.833

AC:

126697

AN:

152124

Hom.:

53210

Cov.:

AF XY:

0.832

AC XY:

61847

AN XY:

74346

show subpopulations

Gnomad4 AFR

AF:

0.714

Gnomad4 AMR

AF:

0.857

Gnomad4 ASJ

AF:

0.879

Gnomad4 EAS

AF:

0.884

Gnomad4 SAS

AF:

0.942

Gnomad4 FIN

AF:

0.815

Gnomad4 NFE

AF:

0.887

Gnomad4 OTH

AF:

0.855

Alfa

AF:

0.882

Hom.:

106386

Bravo

AF:

0.827

Asia WGS

AF:

0.887

AC:

3084

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

1.3

DANN

Benign

0.47

Splicing

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over