Variant chrX-38352177-CTTCT-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP6_Moderate

The NM_001407092.1(OTC):c.-79-436_-79-433delTTCT variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.70 ( 19297 hom., 22310 hem., cov: 0)

Failed GnomAD Quality Control

Consequence

OTC
NM_001407092.1 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.61

Variant links:

Genes affected

ENSG00000250349 (HGNC:):

ENSG00000250349 links:

OTC (HGNC:8512): (ornithine transcarbamylase) This nuclear gene encodes a mitochondrial matrix enzyme. The encoded protein is involved in the urea cycle which functions to detoxify ammonia into urea for excretion. Mutations in this enzyme lead to ornithine transcarbamylase deficiency, which causes hyperammonemia. [provided by RefSeq, May 2022]

OTC links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

BP6

Variant X-38352177-CTTCT-C is Benign according to our data. Variant chrX-38352177-CTTCT-C is described in ClinVar as [Benign]. Clinvar id is 1283242.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chrX-38352177-CTTCT-C is described in Lovd as [Benign].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OTC	NM_001407092.1 linkuse as main transcript	c.-79-436_-79-433delTTCT		intron_variant			NP_001394021.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000250349	ENST00000465127.1 linkuse as main transcript	c.172-313939_172-313936delTTCT		intron_variant		5		ENSP00000417050.1		B4E171

Frequencies

GnomAD3 genomes

AF:

0.699

AC:

76869

AN:

110043

Hom.:

19302

Cov.:

AF XY:

0.688

AC XY:

22266

AN XY:

32367

show subpopulations

Gnomad AFR

AF:

0.668

Gnomad AMI

AF:

0.787

Gnomad AMR

AF:

0.688

Gnomad ASJ

AF:

0.782

Gnomad EAS

AF:

0.720

Gnomad SAS

AF:

0.755

Gnomad FIN

AF:

0.628

Gnomad MID

AF:

0.809

Gnomad NFE

AF:

0.716

Gnomad OTH

AF:

0.679

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

GnomAD4 genome

Data not reliable, filtered out with message: InbreedingCoeff

AF:

0.699

AC:

76905

AN:

110095

Hom.:

19297

Cov.:

AF XY:

0.688

AC XY:

22310

AN XY:

32429

show subpopulations

Gnomad4 AFR

AF:

0.668

Gnomad4 AMR

AF:

0.689

Gnomad4 ASJ

AF:

0.782

Gnomad4 EAS

AF:

0.720

Gnomad4 SAS

AF:

0.753

Gnomad4 FIN

AF:

0.628

Gnomad4 NFE

AF:

0.716

Gnomad4 OTH

AF:

0.679

Alfa

AF:

0.706

Hom.:

5660

Bravo

AF:

0.699

Asia WGS

AF:

0.765

AC:

1926

AN:

2522

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Oct 09, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over