rs1760912
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001042618.2(PARP2):c.903-377A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.45 in 180,134 control chromosomes in the GnomAD database, including 20,273 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 0.46 ( 18148 hom., cov: 32)
Exomes 𝑓: 0.37 ( 2125 hom. )
Consequence
PARP2
NM_001042618.2 intron
NM_001042618.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.615
Genes affected
PARP2 (HGNC:272): (poly(ADP-ribose) polymerase 2) This gene encodes poly(ADP-ribosyl)transferase-like 2 protein, which contains a catalytic domain and is capable of catalyzing a poly(ADP-ribosyl)ation reaction. This protein has a catalytic domain which is homologous to that of poly (ADP-ribosyl) transferase, but lacks an N-terminal DNA binding domain which activates the C-terminal catalytic domain of poly (ADP-ribosyl) transferase. The basic residues within the N-terminal region of this protein may bear potential DNA-binding properties, and may be involved in the nuclear and/or nucleolar targeting of the protein. Two alternatively spliced transcript variants encoding distinct isoforms have been found. [provided by RefSeq, Jul 2008]
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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=-0.97).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.698 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PARP2 | NM_001042618.2 | c.903-377A>T | intron_variant | ENST00000429687.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PARP2 | ENST00000429687.8 | c.903-377A>T | intron_variant | 1 | NM_001042618.2 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.463 AC: 70411AN: 151914Hom.: 18112 Cov.: 32
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GnomAD4 exome AF: 0.374 AC: 10512AN: 28102Hom.: 2125 Cov.: 0 AF XY: 0.373 AC XY: 5539AN XY: 14842
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GnomAD4 genome ? AF: 0.464 AC: 70506AN: 152032Hom.: 18148 Cov.: 32 AF XY: 0.461 AC XY: 34249AN XY: 74322
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ClinVar
Not reported inComputational scores
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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