rs2279216
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_014889.4(PITRM1):c.2917+145C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.245 in 831,298 control chromosomes in the GnomAD database, including 27,138 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 0.20 ( 3898 hom., cov: 34)
Exomes 𝑓: 0.25 ( 23240 hom. )
Consequence
PITRM1
NM_014889.4 intron
NM_014889.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.642
Genes affected
PITRM1 (HGNC:17663): (pitrilysin metallopeptidase 1) The protein encoded by this gene is an ATP-dependent metalloprotease that degrades post-cleavage mitochondrial transit peptides. The encoded protein binds zinc and can also degrade amyloid beta A4 protein, suggesting a possible role in Alzheimer's disease. [provided by RefSeq, Dec 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 (NFE) allele frequency at 95% confidence interval = 0.283 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PITRM1 | NM_014889.4 | c.2917+145C>T | intron_variant | ENST00000224949.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PITRM1 | ENST00000224949.9 | c.2917+145C>T | intron_variant | 1 | NM_014889.4 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.205 AC: 31106AN: 152026Hom.: 3897 Cov.: 34
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GnomAD4 exome AF: 0.254 AC: 172754AN: 679154Hom.: 23240 Cov.: 8 AF XY: 0.255 AC XY: 93471AN XY: 366628
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GnomAD4 genome ? AF: 0.204 AC: 31107AN: 152144Hom.: 3898 Cov.: 34 AF XY: 0.203 AC XY: 15124AN XY: 74388
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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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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at