1-17337985-T-C
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_012387.3(PADI4):c.409-53T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00312 in 997,606 control chromosomes in the GnomAD database, including 60 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.012 ( 35 hom., cov: 32)
Exomes 𝑓: 0.0015 ( 25 hom. )
Consequence
PADI4
NM_012387.3 intron
NM_012387.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -3.82
Genes affected
PADI4 (HGNC:18368): (peptidyl arginine deiminase 4) This gene is a member of a gene family which encodes enzymes responsible for the conversion of arginine residues to citrulline residues. This gene may play a role in granulocyte and macrophage development leading to inflammation and immune response. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0122 (1854/152074) while in subpopulation AFR AF= 0.0414 (1720/41500). AF 95% confidence interval is 0.0398. There are 35 homozygotes in gnomad4. There are 877 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 35 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PADI4 | NM_012387.3 | c.409-53T>C | intron_variant | ENST00000375448.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PADI4 | ENST00000375448.4 | c.409-53T>C | intron_variant | 1 | NM_012387.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0122 AC: 1854AN: 151956Hom.: 35 Cov.: 32
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GnomAD4 exome AF: 0.00149 AC: 1257AN: 845532Hom.: 25 AF XY: 0.00128 AC XY: 570AN XY: 443994
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GnomAD4 genome AF: 0.0122 AC: 1854AN: 152074Hom.: 35 Cov.: 32 AF XY: 0.0118 AC XY: 877AN XY: 74366
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at