chr1-17259639-A-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_016233.2(PADI3):c.154A>G(p.Ile52Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0977 in 1,613,328 control chromosomes in the GnomAD database, including 8,568 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_016233.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PADI3 | NM_016233.2 | c.154A>G | p.Ile52Val | missense_variant | 2/16 | ENST00000375460.3 | |
PADI3 | XM_011541571.3 | c.40A>G | p.Ile14Val | missense_variant | 2/16 | ||
PADI3 | XM_011541572.3 | c.154A>G | p.Ile52Val | missense_variant | 2/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PADI3 | ENST00000375460.3 | c.154A>G | p.Ile52Val | missense_variant | 2/16 | 1 | NM_016233.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0927 AC: 14109AN: 152144Hom.: 696 Cov.: 33
GnomAD3 exomes AF: 0.109 AC: 27311AN: 250788Hom.: 1783 AF XY: 0.113 AC XY: 15300AN XY: 135510
GnomAD4 exome AF: 0.0982 AC: 143513AN: 1461066Hom.: 7870 Cov.: 31 AF XY: 0.101 AC XY: 73618AN XY: 726772
GnomAD4 genome ? AF: 0.0927 AC: 14117AN: 152262Hom.: 698 Cov.: 33 AF XY: 0.0941 AC XY: 7008AN XY: 74452
ClinVar
Submissions by phenotype
PADI3-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Mar 15, 2019 | This variant is classified as 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