chr1-226383047-G-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_001618.4(PARP1):c.1148C>A(p.Ser383Tyr) variant causes a missense change. The variant allele was found at a frequency of 0.00228 in 1,612,654 control chromosomes in the GnomAD database, including 8 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_001618.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PARP1 | NM_001618.4 | c.1148C>A | p.Ser383Tyr | missense_variant | 8/23 | ENST00000366794.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PARP1 | ENST00000366794.10 | c.1148C>A | p.Ser383Tyr | missense_variant | 8/23 | 1 | NM_001618.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00162 AC: 247AN: 152224Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00143 AC: 360AN: 251400Hom.: 2 AF XY: 0.00147 AC XY: 200AN XY: 135890
GnomAD4 exome AF: 0.00234 AC: 3423AN: 1460318Hom.: 8 Cov.: 31 AF XY: 0.00238 AC XY: 1729AN XY: 726440
GnomAD4 genome ? AF: 0.00162 AC: 247AN: 152336Hom.: 0 Cov.: 33 AF XY: 0.00142 AC XY: 106AN XY: 74496
ClinVar
Submissions by phenotype
PARP1-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jul 03, 2020 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at