8-144051440-A-G
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Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The ENST00000618853.5(OPLAH):āc.3753T>Cā(p.Gly1251=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000617 in 1,135,140 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Genomes: not found (cov: 30)
Exomes š: 0.0000062 ( 0 hom. )
Consequence
OPLAH
ENST00000618853.5 synonymous
ENST00000618853.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -4.40
Genes affected
OPLAH (HGNC:8149): (5-oxoprolinase, ATP-hydrolysing) The protein encoded by this gene acts as a homodimer, using ATP hydrolysis to catalyze the conversion of 5-oxo-L-proline to L-glutamate. Defects in this gene are a cause of 5-oxoprolinase deficiency (OPLAHD). [provided by RefSeq, Jun 2012]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.67).
BP6
Variant 8-144051440-A-G is Benign according to our data. Variant chr8-144051440-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 1573775.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-4.4 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
OPLAH | NM_017570.5 | c.3753T>C | p.Gly1251= | synonymous_variant | 27/27 | ENST00000618853.5 | NP_060040.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
OPLAH | ENST00000618853.5 | c.3753T>C | p.Gly1251= | synonymous_variant | 27/27 | 1 | NM_017570.5 | ENSP00000480476 | P1 | |
ENST00000528912.1 | n.1308A>G | non_coding_transcript_exon_variant | 5/5 | 5 |
Frequencies
GnomAD3 genomes Cov.: 30
GnomAD3 genomes
Cov.:
30
GnomAD4 exome AF: 0.00000617 AC: 7AN: 1135140Hom.: 0 Cov.: 37 AF XY: 0.00000360 AC XY: 2AN XY: 555368
GnomAD4 exome
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2
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555368
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GnomAD4 genome Cov.: 30
GnomAD4 genome
Cov.:
30
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
5-Oxoprolinase deficiency Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Aug 09, 2022 | - - |
Computational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at