chr3-122613101-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001113523.3(PARP15):c.604A>G(p.Ile202Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000187 in 1,551,712 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001113523.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PARP15 | NM_001113523.3 | c.604A>G | p.Ile202Val | missense_variant | 4/12 | ENST00000464300.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PARP15 | ENST00000464300.7 | c.604A>G | p.Ile202Val | missense_variant | 4/12 | 1 | NM_001113523.3 | P1 | |
PARP15 | ENST00000483793.5 | c.543+2371A>G | intron_variant | 1 | |||||
PARP15 | ENST00000465304.5 | n.580A>G | non_coding_transcript_exon_variant | 5/14 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152206Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000574 AC: 9AN: 156828Hom.: 0 AF XY: 0.0000602 AC XY: 5AN XY: 82998
GnomAD4 exome AF: 0.0000193 AC: 27AN: 1399506Hom.: 0 Cov.: 31 AF XY: 0.0000232 AC XY: 16AN XY: 690250
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152206Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74350
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 05, 2024 | The c.604A>G (p.I202V) alteration is located in exon 4 (coding exon 4) of the PARP15 gene. This alteration results from a A to G substitution at nucleotide position 604, causing the isoleucine (I) at amino acid position 202 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at