rs3219125
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001618.4(PARP1):c.2406+230A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.059 in 568,548 control chromosomes in the GnomAD database, including 1,187 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 0.051 ( 237 hom., cov: 32)
Exomes 𝑓: 0.062 ( 950 hom. )
Consequence
PARP1
NM_001618.4 intron
NM_001618.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.381
Genes affected
PARP1 (HGNC:270): (poly(ADP-ribose) polymerase 1) This gene encodes a chromatin-associated enzyme, poly(ADP-ribosyl)transferase, which modifies various nuclear proteins by poly(ADP-ribosyl)ation. The modification is dependent on DNA and is involved in the regulation of various important cellular processes such as differentiation, proliferation, and tumor transformation and also in the regulation of the molecular events involved in the recovery of cell from DNA damage. In addition, this enzyme may be the site of mutation in Fanconi anemia, and may participate in the pathophysiology of type I diabetes. [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=-0.82).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0704 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PARP1 | NM_001618.4 | c.2406+230A>G | intron_variant | ENST00000366794.10 | NP_001609.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PARP1 | ENST00000366794.10 | c.2406+230A>G | intron_variant | 1 | NM_001618.4 | ENSP00000355759.5 |
Frequencies
GnomAD3 genomes AF: 0.0509 AC: 7748AN: 152166Hom.: 237 Cov.: 32
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GnomAD4 exome AF: 0.0620 AC: 25805AN: 416264Hom.: 950 Cov.: 4 AF XY: 0.0629 AC XY: 13848AN XY: 220124
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GnomAD4 genome AF: 0.0509 AC: 7744AN: 152284Hom.: 237 Cov.: 32 AF XY: 0.0502 AC XY: 3740AN XY: 74462
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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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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at