rs3219123
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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.2278-39C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0511 in 1,611,774 control chromosomes in the GnomAD database, including 2,511 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 0.040 ( 197 hom., cov: 32)
Exomes 𝑓: 0.052 ( 2314 hom. )
Consequence
PARP1
NM_001618.4 intron
NM_001618.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.489
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=-0.83).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.058 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PARP1 | NM_001618.4 | c.2278-39C>T | intron_variant | ENST00000366794.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PARP1 | ENST00000366794.10 | c.2278-39C>T | intron_variant | 1 | NM_001618.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0403 AC: 6129AN: 152156Hom.: 198 Cov.: 32
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GnomAD3 exomes AF: 0.0445 AC: 11130AN: 250192Hom.: 337 AF XY: 0.0466 AC XY: 6309AN XY: 135332
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GnomAD4 exome AF: 0.0522 AC: 76245AN: 1459500Hom.: 2314 Cov.: 32 AF XY: 0.0529 AC XY: 38394AN XY: 726196
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GnomAD4 genome ? AF: 0.0402 AC: 6128AN: 152274Hom.: 197 Cov.: 32 AF XY: 0.0390 AC XY: 2903AN XY: 74472
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ClinVar
Not reported inComputational scores
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Name
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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