chr1-17249150-A-C
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1
The NM_016233.2(PADI3):c.13A>C(p.Arg5=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0833 in 1,613,938 control chromosomes in the GnomAD database, including 6,665 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.071 ( 473 hom., cov: 32)
Exomes 𝑓: 0.085 ( 6192 hom. )
Consequence
PADI3
NM_016233.2 synonymous
NM_016233.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 3.27
Genes affected
PADI3 (HGNC:18337): (peptidyl arginine deiminase 3) This gene encodes a member of the peptidyl arginine deiminase family of enzymes, which catalyze the post-translational deimination of proteins by converting arginine residues into citrullines in the presence of calcium ions. The family members have distinct substrate specificities and tissue-specific expression patterns. The type III enzyme modulates hair structural proteins, such as filaggrin in the hair follicle and trichohyalin in the inner root sheath, during hair follicle formation. Together with the type I enzyme, this enzyme may also play a role in terminal differentiation of the epidermis. This gene exists in a cluster with four other paralogous genes. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.6).
BP6
?
Variant 1-17249150-A-C is Benign according to our data. Variant chr1-17249150-A-C is described in ClinVar as [Benign]. Clinvar id is 3060112.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=3.27 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.182 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PADI3 | NM_016233.2 | c.13A>C | p.Arg5= | synonymous_variant | 1/16 | ENST00000375460.3 | |
PADI3 | XM_011541572.3 | c.13A>C | p.Arg5= | synonymous_variant | 1/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PADI3 | ENST00000375460.3 | c.13A>C | p.Arg5= | synonymous_variant | 1/16 | 1 | NM_016233.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0715 AC: 10876AN: 152124Hom.: 472 Cov.: 32
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GnomAD3 exomes AF: 0.0972 AC: 24445AN: 251410Hom.: 1548 AF XY: 0.102 AC XY: 13811AN XY: 135878
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GnomAD4 exome AF: 0.0845 AC: 123556AN: 1461696Hom.: 6192 Cov.: 31 AF XY: 0.0877 AC XY: 63800AN XY: 727168
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GnomAD4 genome ? AF: 0.0715 AC: 10883AN: 152242Hom.: 473 Cov.: 32 AF XY: 0.0741 AC XY: 5518AN XY: 74434
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
PADI3-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Mar 15, 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
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BayesDel_noAF
Benign
Cadd
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at