1-17266821-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_016233.2(PADI3):c.511G>A(p.Val171Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0867 in 1,613,246 control chromosomes in the GnomAD database, including 7,208 homozygotes. In-silico tool predicts 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.511G>A | p.Val171Met | missense_variant | 5/16 | ENST00000375460.3 | |
PADI3 | XM_011541571.3 | c.397G>A | p.Val133Met | missense_variant | 5/16 | ||
PADI3 | XM_011541572.3 | c.511G>A | p.Val171Met | missense_variant | 5/12 | ||
PADI3 | XM_017001463.2 | c.-27G>A | 5_prime_UTR_variant | 2/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PADI3 | ENST00000375460.3 | c.511G>A | p.Val171Met | missense_variant | 5/16 | 1 | NM_016233.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0760 AC: 11555AN: 152136Hom.: 533 Cov.: 32
GnomAD3 exomes AF: 0.103 AC: 25982AN: 251216Hom.: 1714 AF XY: 0.109 AC XY: 14735AN XY: 135784
GnomAD4 exome AF: 0.0878 AC: 128257AN: 1460992Hom.: 6675 Cov.: 31 AF XY: 0.0913 AC XY: 66341AN XY: 726884
GnomAD4 genome ? AF: 0.0759 AC: 11558AN: 152254Hom.: 533 Cov.: 32 AF XY: 0.0810 AC XY: 6028AN 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