rs882537

Variant names:

• chr1-17333552-A-G
• rs882537
• NM_012387.3:c.274-391A>G

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 8 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
PADI4	NM_012387.3	c.274-391A>G		intron_variant	Intron 2 of 15	ENST00000375448.4	NP_036519.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PADI4	ENST00000375448.4	c.274-391A>G		intron_variant	Intron 2 of 15	1	NM_012387.3	ENSP00000364597.4
PADI4	ENST00000375453.5	c.274-391A>G		intron_variant	Intron 2 of 3	2		ENSP00000364602.1

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

African (AFR) AF: 0.602 AC: 24736 AN: 41096

American (AMR) AF: 0.601 AC: 9086 AN: 15118

Ashkenazi Jewish (ASJ) AF: 0.671 AC: 2325 AN: 3464

East Asian (EAS) AF: 0.641 AC: 3265 AN: 5094

South Asian (SAS) AF: 0.586 AC: 2791 AN: 4766

European-Finnish (FIN) AF: 0.686 AC: 7146 AN: 10416

Middle Eastern (MID) AF: 0.637 AC: 186 AN: 292

European-Non Finnish (NFE) AF: 0.675 AC: 45752 AN: 67818

Other (OTH) AF: 0.598 AC: 1252 AN: 2094

Alfa AF: 0.660 Hom.: 4325

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
PhyloP100		-0.84
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

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