rs882537

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_012387.3(PADI4):​c.274-391A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.643 in 151,068 control chromosomes in the GnomAD database, including 31,442 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 ( 31442 hom., cov: 27)

Consequence

PADI4
NM_012387.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.845
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]

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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=-0.92).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.669 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
PADI4NM_012387.3 linkuse as main transcriptc.274-391A>G intron_variant ENST00000375448.4

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
PADI4ENST00000375448.4 linkuse as main transcriptc.274-391A>G intron_variant 1 NM_012387.3 P1
PADI4ENST00000375453.5 linkuse as main transcriptc.274-391A>G intron_variant 2

Frequencies

GnomAD3 genomes
AF:
0.643
AC:
97132
AN:
150948
Hom.:
31436
Cov.:
27
show subpopulations
Gnomad AFR
AF:
0.602
Gnomad AMI
AF:
0.701
Gnomad AMR
AF:
0.602
Gnomad ASJ
AF:
0.671
Gnomad EAS
AF:
0.641
Gnomad SAS
AF:
0.587
Gnomad FIN
AF:
0.686
Gnomad MID
AF:
0.621
Gnomad NFE
AF:
0.675
Gnomad OTH
AF:
0.606
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.643
AC:
97177
AN:
151068
Hom.:
31442
Cov.:
27
AF XY:
0.643
AC XY:
47395
AN XY:
73700
show subpopulations
Gnomad4 AFR
AF:
0.602
Gnomad4 AMR
AF:
0.601
Gnomad4 ASJ
AF:
0.671
Gnomad4 EAS
AF:
0.641
Gnomad4 SAS
AF:
0.586
Gnomad4 FIN
AF:
0.686
Gnomad4 NFE
AF:
0.675
Gnomad4 OTH
AF:
0.598
Alfa
AF:
0.662
Hom.:
4188
Bravo
AF:
0.633
Asia WGS
AF:
0.567
AC:
1970
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
0.65
DANN
Benign
0.41

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
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.

Other links and lift over

dbSNP: rs882537; hg19: chr1-17660047; COSMIC: COSV64923452; API