1-17266719-C-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBP6_ModerateBP7BS1BS2_Supporting
The NM_016233.2(PADI3):c.409C>A(p.Arg137Arg) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000541 in 1,612,516 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_016233.2 splice_region, synonymous
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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PADI3 | NM_016233.2 | c.409C>A | p.Arg137Arg | splice_region_variant, synonymous_variant | Exon 5 of 16 | ENST00000375460.3 | NP_057317.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00287 AC: 436AN: 152138Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000632 AC: 158AN: 250008Hom.: 0 AF XY: 0.000488 AC XY: 66AN XY: 135268
GnomAD4 exome AF: 0.000293 AC: 428AN: 1460260Hom.: 1 Cov.: 31 AF XY: 0.000257 AC XY: 187AN XY: 726578
GnomAD4 genome AF: 0.00292 AC: 444AN: 152256Hom.: 3 Cov.: 32 AF XY: 0.00286 AC XY: 213AN XY: 74446
ClinVar
Submissions by phenotype
Inborn genetic diseases Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at