rs11588132
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_012387.3(PADI4):āc.491T>Cā(p.Met164Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000891 in 1,612,974 control chromosomes in the GnomAD database, including 13 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 (ā ). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. M164I) has been classified as Uncertain significance.
Frequency
Consequence
NM_012387.3 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 |
---|---|---|---|---|---|---|---|
PADI4 | NM_012387.3 | c.491T>C | p.Met164Thr | missense_variant | 5/16 | ENST00000375448.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PADI4 | ENST00000375448.4 | c.491T>C | p.Met164Thr | missense_variant | 5/16 | 1 | NM_012387.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00459 AC: 699AN: 152150Hom.: 6 Cov.: 32
GnomAD3 exomes AF: 0.00117 AC: 294AN: 251472Hom.: 2 AF XY: 0.000942 AC XY: 128AN XY: 135910
GnomAD4 exome AF: 0.000503 AC: 735AN: 1460706Hom.: 7 Cov.: 29 AF XY: 0.000442 AC XY: 321AN XY: 726690
GnomAD4 genome ? AF: 0.00461 AC: 702AN: 152268Hom.: 6 Cov.: 32 AF XY: 0.00446 AC XY: 332AN XY: 74462
ClinVar
Submissions by phenotype
PADI4-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jun 05, 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