Variant rs398122026 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1

The ENST00000039007.5(OTC):c.299-34dup variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.15 ( 1383 hom., 4501 hem., cov: 19)

Exomes 𝑓: 0.19 ( 14044 hom. 48998 hem. )

Consequence

OTC
ENST00000039007.5 intron

Scores

Not classified

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.498

Variant links:

Genes affected

OTC (HGNC:8512): (ornithine transcarbamylase) This nuclear gene encodes a mitochondrial matrix enzyme. The encoded protein is involved in the urea cycle which functions to detoxify ammonia into urea for excretion. Mutations in this enzyme lead to ornithine transcarbamylase deficiency, which causes hyperammonemia. [provided by RefSeq, May 2022]

OTC links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP6

Variant X-38381302-G-GT is Benign according to our data. Variant chrX-38381302-G-GT is described in ClinVar as [Likely_benign]. Clinvar id is 256369.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.228 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein
OTC	NM_000531.6 linkuse as main transcript	c.299-34dup	intron_variant	ENST00000039007.5	NP_000522.3
OTC	NM_001407092.1 linkuse as main transcript	c.299-34dup	intron_variant		NP_001394021.1
OTC	XM_017029556.2 linkuse as main transcript	c.299-34dup	intron_variant		XP_016885045.1

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	Appris
OTC	ENST00000039007.5 linkuse as main transcript	c.299-34dup	intron_variant	1	NM_000531.6	ENSP00000039007	P1
OTC	ENST00000643344.1 linkuse as main transcript	c.*49-34dup	intron_variant, NMD_transcript_variant			ENSP00000496606
OTC	ENST00000488812.1 linkuse as main transcript	n.354-52dup	intron_variant, non_coding_transcript_variant	5

Frequencies

GnomAD3 genomes

AF:

0.153

AC:

16831

AN:

110215

Hom.:

1384

Cov.:

AF XY:

0.138

AC XY:

4501

AN XY:

32617

show subpopulations

Gnomad AFR

AF:

0.0364

Gnomad AMI

AF:

0.386

Gnomad AMR

AF:

0.133

Gnomad ASJ

AF:

0.268

Gnomad EAS

AF:

0.000563

Gnomad SAS

AF:

0.0330

Gnomad FIN

AF:

0.143

Gnomad MID

AF:

0.271

Gnomad NFE

AF:

0.232

Gnomad OTH

AF:

0.175

GnomAD3 exomes

AF:

0.152

AC:

22773

AN:

149406

Hom.:

1653

AF XY:

0.154

AC XY:

6930

AN XY:

45084

show subpopulations

Gnomad AFR exome

AF:

0.0329

Gnomad AMR exome

AF:

0.0905

Gnomad ASJ exome

AF:

0.278

Gnomad EAS exome

AF:

0.000346

Gnomad SAS exome

AF:

0.0463

Gnomad FIN exome

AF:

0.165

Gnomad NFE exome

AF:

0.225

Gnomad OTH exome

AF:

0.200

GnomAD4 exome

AF:

0.193

AC:

175662

AN:

908627

Hom.:

14044

Cov.:

AF XY:

0.190

AC XY:

48998

AN XY:

257999

show subpopulations

Gnomad4 AFR exome

AF:

0.0369

Gnomad4 AMR exome

AF:

0.0982

Gnomad4 ASJ exome

AF:

0.277

Gnomad4 EAS exome

AF:

0.000481

Gnomad4 SAS exome

AF:

0.0513

Gnomad4 FIN exome

AF:

0.170

Gnomad4 NFE exome

AF:

0.220

Gnomad4 OTH exome

AF:

0.186

GnomAD4 genome

AF:

0.153

AC:

16821

AN:

110264

Hom.:

1383

Cov.:

AF XY:

0.138

AC XY:

4501

AN XY:

32674

show subpopulations

Gnomad4 AFR

AF:

0.0363

Gnomad4 AMR

AF:

0.133

Gnomad4 ASJ

AF:

0.268

Gnomad4 EAS

AF:

0.000565

Gnomad4 SAS

AF:

0.0324

Gnomad4 FIN

AF:

0.143

Gnomad4 NFE

AF:

0.232

Gnomad4 OTH

AF:

0.174

Alfa

AF:

0.146

Hom.:

1198

Bravo

AF:

0.148

Asia WGS

AF:

0.0370

AC:

AN:

2519

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Mar 03, 2015

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over