chr1-17338127-C-T
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_012387.3(PADI4):c.498C>T(p.Cys166=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000663 in 1,611,552 control chromosomes in the GnomAD database, including 13 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0031 ( 5 hom., cov: 32)
Exomes 𝑓: 0.00041 ( 8 hom. )
Consequence
PADI4
NM_012387.3 synonymous
NM_012387.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.95
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 -11 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BP6
?
Variant 1-17338127-C-T is Benign according to our data. Variant chr1-17338127-C-T is described in ClinVar as [Benign]. Clinvar id is 729596.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-2.95 with no splicing effect.
BS2
?
High Homozygotes in GnomAd at 5 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PADI4 | NM_012387.3 | c.498C>T | p.Cys166= | synonymous_variant | 5/16 | ENST00000375448.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PADI4 | ENST00000375448.4 | c.498C>T | p.Cys166= | synonymous_variant | 5/16 | 1 | NM_012387.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00311 AC: 473AN: 152092Hom.: 5 Cov.: 32
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GnomAD3 exomes AF: 0.000823 AC: 207AN: 251446Hom.: 0 AF XY: 0.000618 AC XY: 84AN XY: 135894
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GnomAD4 exome AF: 0.000407 AC: 594AN: 1459342Hom.: 8 Cov.: 29 AF XY: 0.000368 AC XY: 267AN XY: 726146
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | May 14, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at