rs72633848

Positions:

• chr1-17327880-A-G

Variant summary

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

The NM_012387.3(PADI4):​c.93-3089A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.143 in 151,528 control chromosomes in the GnomAD database, including 2,081 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 0.14 (2081 hom., cov: 31)
• Consequence: PADI4 NM_012387.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01

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=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.205 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PADI4	NM_012387.3	c.93-3089A>G		intron_variant		ENST00000375448.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PADI4	ENST00000375448.4	c.93-3089A>G		intron_variant		1	NM_012387.3	P1
PADI4	ENST00000375453.5	c.93-3089A>G		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.143 AC: 21680 AN: 151412 Hom.: 2082 Cov.: 31

Gnomad AFR AF: 0.0426

Gnomad AMI AF: 0.435

Gnomad AMR AF: 0.111

Gnomad ASJ AF: 0.178

Gnomad EAS AF: 0.00155

Gnomad SAS AF: 0.0869

Gnomad FIN AF: 0.227

Gnomad MID AF: 0.137

Gnomad NFE AF: 0.208

Gnomad OTH AF: 0.139

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.143 AC: 21670 AN: 151528 Hom.: 2081 Cov.: 31 AF XY: 0.142 AC XY: 10479 AN XY: 74022

Gnomad4 AFR AF: 0.0424

Gnomad4 AMR AF: 0.111

Gnomad4 ASJ AF: 0.178

Gnomad4 EAS AF: 0.00155

Gnomad4 SAS AF: 0.0863

Gnomad4 FIN AF: 0.227

Gnomad4 NFE AF: 0.208

Gnomad4 OTH AF: 0.137

Alfa AF: 0.175 Hom.: 339

Bravo AF: 0.128

Asia WGS AF: 0.0450 AC: 159 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.54
DANN	Benign	0.55

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

Other links and lift over

dbSNP: rs72633848; hg19: chr1-17654375; COSMIC: COSV64923371;