rs3093927
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_ModerateBP7BA1
The NM_001042618.2(PARP2):c.891G>A(p.Pro297=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0144 in 1,613,232 control chromosomes in the GnomAD database, including 1,431 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 0.057 ( 757 hom., cov: 32)
Exomes 𝑓: 0.010 ( 674 hom. )
Consequence
PARP2
NM_001042618.2 synonymous
NM_001042618.2 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.179
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 -11 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.42).
BP7
?
Synonymous conserved (PhyloP=-0.179 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.183 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PARP2 | NM_001042618.2 | c.891G>A | p.Pro297= | synonymous_variant | 9/16 | ENST00000429687.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PARP2 | ENST00000429687.8 | c.891G>A | p.Pro297= | synonymous_variant | 9/16 | 1 | NM_001042618.2 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.0570 AC: 8669AN: 152076Hom.: 756 Cov.: 32
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GnomAD3 exomes AF: 0.0178 AC: 4437AN: 248656Hom.: 299 AF XY: 0.0147 AC XY: 1978AN XY: 134912
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GnomAD4 exome AF: 0.00999 AC: 14595AN: 1461038Hom.: 674 Cov.: 31 AF XY: 0.00934 AC XY: 6787AN XY: 726856
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GnomAD4 genome ? AF: 0.0571 AC: 8683AN: 152194Hom.: 757 Cov.: 32 AF XY: 0.0559 AC XY: 4164AN XY: 74432
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Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at