chr1-17373182-G-A
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Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 2P and 11B. PM2BP4_StrongBP6_ModerateBP7BS1
The NM_207421.4(PADI6):c.243G>A(p.Thr81=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000693 in 1,613,970 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00056 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00071 ( 0 hom. )
Consequence
PADI6
NM_207421.4 synonymous
NM_207421.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.213
Genes affected
PADI6 (HGNC:20449): (peptidyl arginine deiminase 6) 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. This protein may play a role in cytoskeletal reorganization in the egg and in early embryo development. [provided by RefSeq, Sep 2012]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -9 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BP6
Variant 1-17373182-G-A is Benign according to our data. Variant chr1-17373182-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 1334958.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.213 with no splicing effect.
BS1
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.000565 (86/152280) while in subpopulation NFE AF= 0.0011 (75/68028). AF 95% confidence interval is 0.000902. There are 0 homozygotes in gnomad4. There are 36 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PADI6 | NM_207421.4 | c.243G>A | p.Thr81= | synonymous_variant | 2/16 | ENST00000619609.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PADI6 | ENST00000619609.1 | c.243G>A | p.Thr81= | synonymous_variant | 2/16 | 1 | NM_207421.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000559 AC: 85AN: 152162Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000470 AC: 117AN: 249136Hom.: 0 AF XY: 0.000436 AC XY: 59AN XY: 135172
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GnomAD4 exome AF: 0.000706 AC: 1032AN: 1461690Hom.: 0 Cov.: 31 AF XY: 0.000704 AC XY: 512AN XY: 727134
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GnomAD4 genome AF: 0.000565 AC: 86AN: 152280Hom.: 0 Cov.: 32 AF XY: 0.000483 AC XY: 36AN XY: 74462
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ClinVar
Significance: Likely benign
Submissions summary: Benign:2
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
PADI6-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Aug 03, 2020 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Mar 01, 2023 | PADI6: BP4, BP7 - |
Computational scores
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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