chr1-17331112-C-G
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_012387.3(PADI4):c.236C>G(p.Thr79Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000298 in 1,611,980 control chromosomes in the GnomAD database, including 5 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 variant affecting the same amino acid position, but resulting in a different missense (i.e. T79M) has been classified as Benign.
Frequency
Consequence
NM_012387.3 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 |
---|---|---|---|---|---|---|---|
PADI4 | NM_012387.3 | c.236C>G | p.Thr79Arg | missense_variant | 2/16 | ENST00000375448.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PADI4 | ENST00000375448.4 | c.236C>G | p.Thr79Arg | missense_variant | 2/16 | 1 | NM_012387.3 | P1 | |
PADI4 | ENST00000375453.5 | c.236C>G | p.Thr79Arg | missense_variant | 2/4 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.000421 AC: 64AN: 152144Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000962 AC: 239AN: 248398Hom.: 4 AF XY: 0.000879 AC XY: 118AN XY: 134292
GnomAD4 exome AF: 0.000286 AC: 417AN: 1459718Hom.: 5 Cov.: 37 AF XY: 0.000273 AC XY: 198AN XY: 726112
GnomAD4 genome ? AF: 0.000420 AC: 64AN: 152262Hom.: 0 Cov.: 33 AF XY: 0.000443 AC XY: 33AN XY: 74434
ClinVar
Submissions by phenotype
PADI4-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Dec 06, 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