rs2305666
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_018622.7(PARL):c.829-120T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.188 in 731,038 control chromosomes in the GnomAD database, including 14,470 homozygotes. 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 0.19 ( 3014 hom., cov: 32)
Exomes 𝑓: 0.19 ( 11456 hom. )
Consequence
PARL
NM_018622.7 intron
NM_018622.7 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.669
Genes affected
PARL (HGNC:18253): (presenilin associated rhomboid like) This gene encodes a member of the rhomboid family of intramembrane serine proteases that is localized to the inner mitochondrial membrane. The encoded protein regulates mitochondrial remodeling and apoptosis through regulated substrate proteolysis. Proteolytic processing of the encoded protein results in the release of a small peptide, P-beta, which may transit to the nucleus. Mutations in this gene may be associated with Parkinson's disease. [provided by RefSeq, May 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.414 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PARL | NM_018622.7 | c.829-120T>G | intron_variant | ENST00000317096.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PARL | ENST00000317096.9 | c.829-120T>G | intron_variant | 1 | NM_018622.7 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.192 AC: 29159AN: 152098Hom.: 2993 Cov.: 32
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GnomAD4 exome AF: 0.187 AC: 107980AN: 578822Hom.: 11456 AF XY: 0.184 AC XY: 57309AN XY: 311590
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GnomAD4 genome ? AF: 0.192 AC: 29216AN: 152216Hom.: 3014 Cov.: 32 AF XY: 0.191 AC XY: 14219AN XY: 74420
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ClinVar
Not reported inComputational 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