chrX-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 NM_001407092.1(OTC):​c.-79-436_-79-433del 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
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.61

Genes affected

OTC (HGNC:):

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	UniProt
OTC	NM_001407092.1	c.-79-436_-79-433del		intron_variant

Ensembl

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

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;