X-38352177-CTTCT-C

Position:

• chrX-38352177-CTTCT-C

Variant summary

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

The ENST00000465127.1(ENSG00000250349):​c.172-313939_172-313936delTTCT 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: ENSG00000250349 ENST00000465127.1 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.61

Genes affected

ENSG00000250349 (HGNC:):

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]

ACMG classification

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	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	c.172-313939_172-313936delTTCT		intron_variant		5		ENSP00000417050.1

Frequencies

GnomAD3 genomes AF: 0.699 AC: 76869 AN: 110043 Hom.: 19302 Cov.: 0 AF XY: 0.688 AC XY: 22266 AN XY: 32367

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.: 0 AF XY: 0.688 AC XY: 22310 AN XY: 32429

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

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Oct 09, 2018

- -

Computational scores

Source: dbNSFP v4.3

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: rs57752938; hg19: chrX-38211430;