chrX-38352036-C-T

Position:

• chrX-38352036-C-T

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_Strong BP6_Moderate

The NM_001407092.1(OTC):​c.-79-582C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.71 (19549 hom., 23366 hem., cov: 24)
  • Failed GnomAD Quality Control
• Consequence: OTC NM_001407092.1 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -3.21

Genes affected

OTC (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -6 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BP6: Variant X-38352036-C-T is Benign according to our data. Variant chrX-38352036-C-T is described in ClinVar as [Benign]. Clinvar id is 680700.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OTC	NM_001407092.1	c.-79-582C>T		intron_variant			NP_001394021.1

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.705 AC: 78276 AN: 110957 Hom.: 19555 Cov.: 24 AF XY: 0.700 AC XY: 23321 AN XY: 33323

Gnomad AFR AF: 0.687

Gnomad AMI AF: 0.790

Gnomad AMR AF: 0.694

Gnomad ASJ AF: 0.781

Gnomad EAS AF: 0.725

Gnomad SAS AF: 0.764

Gnomad FIN AF: 0.634

Gnomad MID AF: 0.809

Gnomad NFE AF: 0.717

Gnomad OTH AF: 0.683

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: 0.705 AC: 78312 AN: 111013 Hom.: 19549 Cov.: 24 AF XY: 0.700 AC XY: 23366 AN XY: 33389

Gnomad4 AFR AF: 0.687

Gnomad4 AMR AF: 0.694

Gnomad4 ASJ AF: 0.781

Gnomad4 EAS AF: 0.724

Gnomad4 SAS AF: 0.762

Gnomad4 FIN AF: 0.634

Gnomad4 NFE AF: 0.717

Gnomad4 OTH AF: 0.684

Alfa AF: 0.709 Hom.: 5695

Bravo AF: 0.705

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

Jun 14, 2018

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. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.86
DANN	Benign	0.33

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: rs5963412; hg19: chrX-38211289;