chr3-122610540-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001113523.3(PARP15):c.353G>A(p.Gly118Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000348 in 1,551,574 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.353G>A | p.Gly118Glu | missense_variant | 3/12 | ENST00000464300.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PARP15 | ENST00000464300.7 | c.353G>A | p.Gly118Glu | missense_variant | 3/12 | 1 | NM_001113523.3 | P1 | |
PARP15 | ENST00000483793.5 | c.353G>A | p.Gly118Glu | missense_variant | 3/9 | 1 | |||
PARP15 | ENST00000465304.5 | n.329G>A | non_coding_transcript_exon_variant | 4/14 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152166Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.0000364 AC: 51AN: 1399408Hom.: 0 Cov.: 30 AF XY: 0.0000391 AC XY: 27AN XY: 690212
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152166Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74324
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 18, 2021 | The c.353G>A (p.G118E) alteration is located in exon 3 (coding exon 3) of the PARP15 gene. This alteration results from a G to A substitution at nucleotide position 353, causing the glycine (G) at amino acid position 118 to be replaced by a glutamic acid (E). 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