rs1223118
Positions:
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1
The NM_001304274.2(IMMP1L):c.321+7307C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0207 in 985,216 control chromosomes in the GnomAD database, including 2,314 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 0.088 ( 1636 hom., cov: 32)
Exomes 𝑓: 0.0083 ( 678 hom. )
Consequence
IMMP1L
NM_001304274.2 intron
NM_001304274.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.12
Genes affected
IMMP1L (HGNC:26317): (inner mitochondrial membrane peptidase subunit 1) The mitochondrial inner membrane peptidase (IMP) complex generates mature, active proteins in the mitochondrial intermembrane space by proteolytically removing the mitochondrial targeting presequence of nuclear-encoded proteins. IMP1 and IMP2 (IMMP2L; MIM 605977) are the catalytic subunits of the IMP complex (Burri et al., 2005 [PubMed 15814844]).[supplied by OMIM, Sep 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.38).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.266 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IMMP1L | NM_001304274.2 | c.321+7307C>G | intron_variant | ENST00000532287.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IMMP1L | ENST00000532287.6 | c.321+7307C>G | intron_variant | 1 | NM_001304274.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0882 AC: 13404AN: 152042Hom.: 1629 Cov.: 32
GnomAD3 genomes
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GnomAD4 exome AF: 0.00830 AC: 6914AN: 833056Hom.: 678 Cov.: 30 AF XY: 0.00768 AC XY: 2953AN XY: 384688
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GnomAD4 genome ? AF: 0.0884 AC: 13458AN: 152160Hom.: 1636 Cov.: 32 AF XY: 0.0861 AC XY: 6406AN XY: 74394
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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