rs2240337

chr1-17347727-C-T

Variant summary

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

The NM_012387.3(PADI4):c.1048-214C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0944 in 152,252 control chromosomes in the GnomAD database, including 768 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 0.094 (768 hom., cov: 33)
• Consequence: PADI4 NM_012387.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.114

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=-0.8).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.118 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PADI4	NM_012387.3	c.1048-214C>T		intron_variant		ENST00000375448.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PADI4	ENST00000375448.4	c.1048-214C>T		intron_variant		1	NM_012387.3	P1
PADI4	ENST00000468945.1	n.107-214C>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.0943 AC: 14348 AN: 152134 Hom.: 764 Cov.: 33

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.0406

Gnomad AMR AF: 0.121

Gnomad ASJ AF: 0.0856

Gnomad EAS AF: 0.0658

Gnomad SAS AF: 0.0244

Gnomad FIN AF: 0.0773

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.0820

Gnomad OTH AF: 0.109

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

GnomAD4 genome AF: 0.0944 AC: 14371 AN: 152252 Hom.: 768 Cov.: 33 AF XY: 0.0927 AC XY: 6900 AN XY: 74450

Gnomad4 AFR AF: 0.121

Gnomad4 AMR AF: 0.122

Gnomad4 ASJ AF: 0.0856

Gnomad4 EAS AF: 0.0665

Gnomad4 SAS AF: 0.0245

Gnomad4 FIN AF: 0.0773

Gnomad4 NFE AF: 0.0820

Gnomad4 OTH AF: 0.108

Alfa AF: 0.0835 Hom.: 712

Bravo AF: 0.100

Asia WGS AF: 0.0680 AC: 236 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
Cadd	Benign	2.4
Dann	Benign	0.89

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: rs2240337; hg19: chr1-17674222;