Variant 1-17331039-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_012387.3(PADI4):c.163G>A(p.Gly55Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.574 in 1,607,640 control chromosomes in the GnomAD database, including 266,699 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.55 ( 23311 hom., cov: 32)

Exomes 𝑓: 0.58 ( 243388 hom. )

Consequence

PADI4
NM_012387.3 missense

Scores

Clinical Significance

Benign criteria provided, single submitter B:1O:1

Conservation

PhyloP100: -1.24

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=1.2175569E-5).

BP6

Variant 1-17331039-G-A is Benign according to our data. Variant chr1-17331039-G-A is described in ClinVar as [Benign]. Clinvar id is 972892.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.579 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PADI4	NM_012387.3 linkuse as main transcript	c.163G>A	p.Gly55Ser	missense_variant	2/16	ENST00000375448.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PADI4	ENST00000375448.4 linkuse as main transcript	c.163G>A	p.Gly55Ser	missense_variant	2/16	1	NM_012387.3	P1
PADI4	ENST00000375453.5 linkuse as main transcript	c.163G>A	p.Gly55Ser	missense_variant	2/4	2

Frequencies

GnomAD3 genomes

AF:

0.551

AC:

83654

AN:

151870

Hom.:

23320

Cov.:

show subpopulations

Gnomad AFR

AF:

0.476

Gnomad AMI

AF:

0.649

Gnomad AMR

AF:

0.548

Gnomad ASJ

AF:

0.618

Gnomad EAS

AF:

0.593

Gnomad SAS

AF:

0.532

Gnomad FIN

AF:

0.593

Gnomad MID

AF:

0.576

Gnomad NFE

AF:

0.584

Gnomad OTH

AF:

0.531

GnomAD3 exomes

AF:

0.559

AC:

137546

AN:

246090

Hom.:

38920

AF XY:

0.563

AC XY:

74936

AN XY:

133190

show subpopulations

Gnomad AFR exome

AF:

0.471

Gnomad AMR exome

AF:

0.500

Gnomad ASJ exome

AF:

0.595

Gnomad EAS exome

AF:

0.577

Gnomad SAS exome

AF:

0.522

Gnomad FIN exome

AF:

0.590

Gnomad NFE exome

AF:

0.586

Gnomad OTH exome

AF:

0.571

GnomAD4 exome

AF:

0.577

AC:

839624

AN:

1455652

Hom.:

243388

Cov.:

AF XY:

0.576

AC XY:

417280

AN XY:

724128

show subpopulations

Gnomad4 AFR exome

AF:

0.471

Gnomad4 AMR exome

AF:

0.513

Gnomad4 ASJ exome

AF:

0.604

Gnomad4 EAS exome

AF:

0.592

Gnomad4 SAS exome

AF:

0.528

Gnomad4 FIN exome

AF:

0.587

Gnomad4 NFE exome

AF:

0.586

Gnomad4 OTH exome

AF:

0.559

GnomAD4 genome

AF:

0.551

AC:

83679

AN:

151988

Hom.:

23311

Cov.:

AF XY:

0.551

AC XY:

40952

AN XY:

74292

show subpopulations

Gnomad4 AFR

AF:

0.476

Gnomad4 AMR

AF:

0.548

Gnomad4 ASJ

AF:

0.618

Gnomad4 EAS

AF:

0.593

Gnomad4 SAS

AF:

0.531

Gnomad4 FIN

AF:

0.593

Gnomad4 NFE

AF:

0.584

Gnomad4 OTH

AF:

0.524

Alfa

AF:

0.579

Hom.:

62092

Bravo

AF:

0.543

TwinsUK

AF:

0.586

AC:

2174

ALSPAC

AF:

0.591

AC:

2279

ESP6500AA

AF:

0.485

AC:

2135

ESP6500EA

AF:

0.577

AC:

4958

ExAC

AF:

0.561

AC:

68108

Asia WGS

AF:

0.484

AC:

1682

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1Other:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

PADI4-related disorder

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

Oct 17, 2019

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). -

Rheumatoid arthritis;C5441745:Abnormal pulmonary interstitial morphology

Other:1

association, no assertion criteria provided

case-control

HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosio Villegas

Feb 01, 2020

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.071

BayesDel_addAF

Benign

-0.91

BayesDel_noAF

Benign

-0.93

Cadd

Benign

0.0020

Dann

Benign

0.48

DEOGEN2

Benign

0.0036

T;T

Eigen

Benign

-2.1

Eigen_PC

Benign

-2.1

FATHMM_MKL

Benign

0.0051

MetaRNN

Benign

0.000012

T;T

MetaSVM

Benign

-0.91

MutationTaster

Benign

1.0

P;P

PrimateAI

Benign

0.20

PROVEAN

Benign

1.5

N;N

REVEL

Benign

0.025

Sift

Benign

1.0

T;T

Sift4G

Benign

0.80

T;T

Polyphen

0.0

.;B

Vest4

0.022

MPC

0.11

ClinPred

0.042

GERP RS

-11

Varity_R

0.038

gMVP

0.13

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

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