X-38352332-G-A

Position:

• chrX-38352332-G-A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_001407092.1(OTC):​c.-79-286G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.134 in 111,471 control chromosomes in the GnomAD database, including 807 homozygotes. There are 4,317 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.13 (807 hom., 4317 hem., cov: 24)
• Consequence: OTC NM_001407092.1 intron
• Clinical Significance: Benign criteria provided, single submitter B:2
• Conservation: PhyloP100: 0.552

Genes affected

OTC (HGNC:):

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BP6: Variant X-38352332-G-A is Benign according to our data. Variant chrX-38352332-G-A is described in ClinVar as [Benign]. Clinvar id is 380178.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.165 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
OTC	NM_001407092.1	c.-79-286G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.134 AC: 14878 AN: 111418 Hom.: 806 Cov.: 24 AF XY: 0.128 AC XY: 4306 AN XY: 33624

Gnomad AFR AF: 0.0877

Gnomad AMI AF: 0.127

Gnomad AMR AF: 0.101

Gnomad ASJ AF: 0.170

Gnomad EAS AF: 0.0581

Gnomad SAS AF: 0.165

Gnomad FIN AF: 0.141

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.168

Gnomad OTH AF: 0.115

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

GnomAD4 genome AF: 0.134 AC: 14890 AN: 111471 Hom.: 807 Cov.: 24 AF XY: 0.128 AC XY: 4317 AN XY: 33687

Gnomad4 AFR AF: 0.0878

Gnomad4 AMR AF: 0.101

Gnomad4 ASJ AF: 0.170

Gnomad4 EAS AF: 0.0583

Gnomad4 SAS AF: 0.166

Gnomad4 FIN AF: 0.141

Gnomad4 NFE AF: 0.168

Gnomad4 OTH AF: 0.112

Alfa AF: 0.153 Hom.: 1306

Bravo AF: 0.125

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Dec 02, 2015

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

Ornithine carbamoyltransferase deficiency Benign:1

Benign, no assertion criteria provided

clinical testing

Natera, Inc.

Sep 16, 2020

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	8.3
DANN	Benign	0.70

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: rs5963030; hg19: chrX-38211585;