rs957415
Positions:
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_000531.6(OTC):c.663+50A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0042 in 1,164,513 control chromosomes in the GnomAD database, including 9 homozygotes. There are 1,613 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0030 ( 1 hom., 97 hem., cov: 23)
Exomes 𝑓: 0.0043 ( 8 hom. 1516 hem. )
Consequence
OTC
NM_000531.6 intron
NM_000531.6 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.209
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BP6
?
Variant X-38403790-A-G is Benign according to our data. Variant chrX-38403790-A-G is described in ClinVar as [Benign]. Clinvar id is 256371.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.00297 (332/111823) while in subpopulation NFE AF= 0.00485 (258/53158). AF 95% confidence interval is 0.00437. There are 1 homozygotes in gnomad4. There are 97 alleles in male gnomad4 subpopulation. Median coverage is 23. This position pass quality control queck.
BS2
?
High Hemizygotes in GnomAd4 at 97 XL gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OTC | NM_000531.6 | c.663+50A>G | intron_variant | ENST00000039007.5 | |||
OTC | NM_001407092.1 | c.663+50A>G | intron_variant | ||||
OTC | XM_017029556.2 | c.663+50A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OTC | ENST00000039007.5 | c.663+50A>G | intron_variant | 1 | NM_000531.6 | P1 | |||
OTC | ENST00000643344.1 | c.*413+50A>G | intron_variant, NMD_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.00297 AC: 332AN: 111770Hom.: 1 Cov.: 23 AF XY: 0.00286 AC XY: 97AN XY: 33956
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GnomAD3 exomes AF: 0.00275 AC: 498AN: 180767Hom.: 1 AF XY: 0.00326 AC XY: 215AN XY: 65993
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GnomAD4 exome AF: 0.00433 AC: 4558AN: 1052690Hom.: 8 Cov.: 25 AF XY: 0.00470 AC XY: 1516AN XY: 322506
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GnomAD4 genome ? AF: 0.00297 AC: 332AN: 111823Hom.: 1 Cov.: 23 AF XY: 0.00285 AC XY: 97AN XY: 34019
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at