1-17070197-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_007365.3(PADI2):c.1655G>A(p.Arg552His) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000359 in 1,614,020 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_007365.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PADI2 | ENST00000375486.9 | c.1655G>A | p.Arg552His | missense_variant | Exon 15 of 16 | 1 | NM_007365.3 | ENSP00000364635.4 | ||
PADI2 | ENST00000466151.1 | n.2011G>A | non_coding_transcript_exon_variant | Exon 6 of 7 | 2 | |||||
PADI2 | ENST00000479534.5 | n.602G>A | non_coding_transcript_exon_variant | Exon 3 of 4 | 2 |
Frequencies
GnomAD3 genomes AF: 0.000112 AC: 17AN: 152158Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000517 AC: 13AN: 251272Hom.: 0 AF XY: 0.0000589 AC XY: 8AN XY: 135792
GnomAD4 exome AF: 0.0000280 AC: 41AN: 1461744Hom.: 0 Cov.: 31 AF XY: 0.0000303 AC XY: 22AN XY: 727192
GnomAD4 genome AF: 0.000112 AC: 17AN: 152276Hom.: 0 Cov.: 32 AF XY: 0.0000940 AC XY: 7AN XY: 74456
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1655G>A (p.R552H) alteration is located in exon 15 (coding exon 15) of the PADI2 gene. This alteration results from a G to A substitution at nucleotide position 1655, causing the arginine (R) at amino acid position 552 to be replaced by a histidine (H). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at