rs5963411

chrX-38351864-G-AchrX-38351864-G-C

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_Strong BS2

The NM_001407092.1(OTC):c.-79-754G>A 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 (19518 hom., 22899 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: OTC NM_001407092.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.903

Genes affected

OTC (HGNC:):

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BS2: High Homozygotes in GnomAd at 19524 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
OTC	NM_001407092.1	c.-79-754G>A		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.706 AC: 77750 AN: 110147 Hom.: 19524 Cov.: 23 AF XY: 0.701 AC XY: 22854 AN XY: 32589

Gnomad AFR AF: 0.687

Gnomad AMI AF: 0.789

Gnomad AMR AF: 0.693

Gnomad ASJ AF: 0.781

Gnomad EAS AF: 0.723

Gnomad SAS AF: 0.767

Gnomad FIN AF: 0.641

Gnomad MID AF: 0.813

Gnomad NFE AF: 0.718

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: 0.706 AC: 77786 AN: 110201 Hom.: 19518 Cov.: 23 AF XY: 0.701 AC XY: 22899 AN XY: 32653

Gnomad4 AFR AF: 0.687

Gnomad4 AMR AF: 0.694

Gnomad4 ASJ AF: 0.781

Gnomad4 EAS AF: 0.723

Gnomad4 SAS AF: 0.765

Gnomad4 FIN AF: 0.641

Gnomad4 NFE AF: 0.718

Gnomad4 OTH AF: 0.683

Alfa AF: 0.699 Hom.: 5335

Bravo AF: 0.705

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.60
Dann	Benign	0.55

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: rs5963411; hg19: chrX-38211117;