X-38351716-A-G

Position:

• chrX-38351716-A-G

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The NM_001407092.1(OTC):​c.-79-902A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.71 (19980 hom., 22990 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: OTC NM_001407092.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.384

Genes affected

OTC (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OTC	NM_001407092.1	c.-79-902A>G		intron_variant			NP_001394021.1

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.712 AC: 78567 AN: 110374 Hom.: 19988 Cov.: 23 AF XY: 0.704 AC XY: 22946 AN XY: 32576

Gnomad AFR AF: 0.709

Gnomad AMI AF: 0.787

Gnomad AMR AF: 0.695

Gnomad ASJ AF: 0.781

Gnomad EAS AF: 0.725

Gnomad SAS AF: 0.768

Gnomad FIN AF: 0.635

Gnomad MID AF: 0.811

Gnomad NFE AF: 0.718

Gnomad OTH AF: 0.689

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: 0.712 AC: 78600 AN: 110427 Hom.: 19980 Cov.: 23 AF XY: 0.704 AC XY: 22990 AN XY: 32639

Gnomad4 AFR AF: 0.709

Gnomad4 AMR AF: 0.696

Gnomad4 ASJ AF: 0.781

Gnomad4 EAS AF: 0.725

Gnomad4 SAS AF: 0.765

Gnomad4 FIN AF: 0.635

Gnomad4 NFE AF: 0.718

Gnomad4 OTH AF: 0.690

Alfa AF: 0.530 Hom.: 2068

Bravo AF: 0.712

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.90
DANN	Benign	0.51

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: rs5963409; hg19: chrX-38210969;