Genetic Variant PADI4:p.Arg383Arg (chr1-17348042-C-A) – ACMG Classification: Benign (-14 pts)

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BA1

The NM_012387.3(PADI4):c.1149C>A(p.Arg383Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.364 in 1,587,424 control chromosomes in the GnomAD database, including 107,661 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.37 ( 10786 hom., cov: 31)

Exomes 𝑓: 0.36 ( 96875 hom. )

Consequence

PADI4
NM_012387.3 synonymous

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: -3.32

Variant links:

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]

PADI4 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.65).

BP6

Variant 1-17348042-C-A is Benign according to our data. Variant chr1-17348042-C-A is described in ClinVar as [Benign]. Clinvar id is 3059475.Status of the report is no_assertion_criteria_provided, 0 stars.

BP7

Synonymous conserved (PhyloP=-3.32 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.572 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PADI4	NM_012387.3 link	c.1149C>A	p.Arg383Arg	synonymous_variant	Exon 10 of 16	ENST00000375448.4	NP_036519.2	Q9UM07

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
PADI4	ENST00000375448.4 link	c.1149C>A	p.Arg383Arg	synonymous_variant	Exon 10 of 16	1	NM_012387.3	ENSP00000364597.4	Q9UM07
PADI4	ENST00000468945.1 link	n.208C>A		non_coding_transcript_exon_variant	Exon 2 of 2	2
PADI4	ENST00000487048.5 link	n.116C>A		non_coding_transcript_exon_variant	Exon 1 of 4	3

Frequencies

GnomAD3 genomes

AF:

0.372

AC:

56417

AN:

151764

Hom.:

10789

Cov.:

show subpopulations

Gnomad AFR

AF:

0.367

Gnomad AMI

AF:

0.198

Gnomad AMR

AF:

0.418

Gnomad ASJ

AF:

0.423

Gnomad EAS

AF:

0.589

Gnomad SAS

AF:

0.452

Gnomad FIN

AF:

0.333

Gnomad MID

AF:

0.440

Gnomad NFE

AF:

0.348

Gnomad OTH

AF:

0.364

GnomAD3 exomes

AF:

0.389

AC:

97177

AN:

249762

Hom.:

19741

AF XY:

0.391

AC XY:

52813

AN XY:

135028

show subpopulations

Gnomad AFR exome

AF:

0.373

Gnomad AMR exome

AF:

0.410

Gnomad ASJ exome

AF:

0.415

Gnomad EAS exome

AF:

0.583

Gnomad SAS exome

AF:

0.436

Gnomad FIN exome

AF:

0.335

Gnomad NFE exome

AF:

0.349

Gnomad OTH exome

AF:

0.383

GnomAD4 exome

AF:

0.363

AC:

520593

AN:

1435542

Hom.:

96875

Cov.:

AF XY:

0.365

AC XY:

261546

AN XY:

715620

show subpopulations

Gnomad4 AFR exome

AF:

0.370

Gnomad4 AMR exome

AF:

0.418

Gnomad4 ASJ exome

AF:

0.417

Gnomad4 EAS exome

AF:

0.584

Gnomad4 SAS exome

AF:

0.439

Gnomad4 FIN exome

AF:

0.333

Gnomad4 NFE exome

AF:

0.346

Gnomad4 OTH exome

AF:

0.372

GnomAD4 genome

AF:

0.372

AC:

56442

AN:

151882

Hom.:

10786

Cov.:

AF XY:

0.375

AC XY:

27827

AN XY:

74216

show subpopulations

Gnomad4 AFR

AF:

0.367

Gnomad4 AMR

AF:

0.418

Gnomad4 ASJ

AF:

0.423

Gnomad4 EAS

AF:

0.589

Gnomad4 SAS

AF:

0.451

Gnomad4 FIN

AF:

0.333

Gnomad4 NFE

AF:

0.348

Gnomad4 OTH

AF:

0.359

Alfa

AF:

0.363

Hom.:

17472

Bravo

AF:

0.380

Asia WGS

AF:

0.441

AC:

1529

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

PADI4-related disorder

Benign:1

Oct 17, 2019

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

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

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.65

CADD

Benign

1.0

DANN

Benign

0.83

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over