rs34309058
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_012387.3(PADI4):c.304C>A(p.Pro102Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0149 in 1,612,530 control chromosomes in the GnomAD database, including 241 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_012387.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PADI4 | NM_012387.3 | c.304C>A | p.Pro102Thr | missense_variant | 3/16 | ENST00000375448.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PADI4 | ENST00000375448.4 | c.304C>A | p.Pro102Thr | missense_variant | 3/16 | 1 | NM_012387.3 | P1 | |
PADI4 | ENST00000375453.5 | c.304C>A | p.Pro102Thr | missense_variant | 3/4 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0110 AC: 1666AN: 152122Hom.: 16 Cov.: 30
GnomAD3 exomes AF: 0.0108 AC: 2715AN: 251444Hom.: 25 AF XY: 0.0109 AC XY: 1482AN XY: 135898
GnomAD4 exome AF: 0.0153 AC: 22337AN: 1460290Hom.: 225 Cov.: 28 AF XY: 0.0149 AC XY: 10800AN XY: 726548
GnomAD4 genome ? AF: 0.0109 AC: 1666AN: 152240Hom.: 16 Cov.: 30 AF XY: 0.0105 AC XY: 780AN XY: 74432
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at