rs882537

Positions:

• chr1-17333552-A-G
• chr1-17333552-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.845

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]

ACMG classification

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
PADI4	NM_012387.3	c.274-391A>G		intron_variant		ENST00000375448.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PADI4	ENST00000375448.4	c.274-391A>G		intron_variant		1	NM_012387.3	P1
PADI4	ENST00000375453.5	c.274-391A>G		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.643 AC: 97132 AN: 150948 Hom.: 31436 Cov.: 27

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

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

Other links and lift over

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