chr1-17336256-C-G
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_012387.3(PADI4):c.408+30C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.662 in 1,587,572 control chromosomes in the GnomAD database, including 349,626 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 0.64 ( 31665 hom., cov: 33)
Exomes 𝑓: 0.66 ( 317961 hom. )
Consequence
PADI4
NM_012387.3 intron
NM_012387.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0920
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=-0.98).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.67 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PADI4 | NM_012387.3 | c.408+30C>G | intron_variant | ENST00000375448.4 | NP_036519.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PADI4 | ENST00000375448.4 | c.408+30C>G | intron_variant | 1 | NM_012387.3 | ENSP00000364597.4 |
Frequencies
GnomAD3 genomes AF: 0.643 AC: 97787AN: 152028Hom.: 31656 Cov.: 33
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GnomAD3 exomes AF: 0.634 AC: 157977AN: 249002Hom.: 50678 AF XY: 0.637 AC XY: 85732AN XY: 134558
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GnomAD4 exome AF: 0.664 AC: 952515AN: 1435426Hom.: 317961 Cov.: 26 AF XY: 0.662 AC XY: 473576AN XY: 715640
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GnomAD4 genome AF: 0.643 AC: 97835AN: 152146Hom.: 31665 Cov.: 33 AF XY: 0.643 AC XY: 47819AN XY: 74374
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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