chr1-17347613-C-T

Variant names:

• chr1-17347613-C-T
• rs2240339
• NM_012387.3:c.1048-328C>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.1048-328C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.366 in 151,210 control chromosomes in the GnomAD database, including 10,470 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 0.37 (10470 hom., cov: 29)
• Consequence: PADI4 NM_012387.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.363
• Publications: 20 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.57 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_012387.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PADI4	NM_012387.3	MANE Select	c.1048-328C>T		intron	N/A	NP_036519.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PADI4	ENST00000375448.4	TSL:1 MANE Select	c.1048-328C>T		intron	N/A	ENSP00000364597.4
	PADI4	ENST00000468945.1	TSL:2	n.107-328C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.367 AC: 55393 AN: 151092 Hom.: 10473 Cov.: 29

Gnomad AFR AF: 0.352

Gnomad AMI AF: 0.195

Gnomad AMR AF: 0.416

Gnomad ASJ AF: 0.423

Gnomad EAS AF: 0.587

Gnomad SAS AF: 0.451

Gnomad FIN AF: 0.330

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.347

Gnomad OTH AF: 0.361

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

GnomAD4 genome AF: 0.366 AC: 55418 AN: 151210 Hom.: 10470 Cov.: 29 AF XY: 0.370 AC XY: 27308 AN XY: 73810

African (AFR) AF: 0.352 AC: 14493 AN: 41178

American (AMR) AF: 0.416 AC: 6319 AN: 15194

Ashkenazi Jewish (ASJ) AF: 0.423 AC: 1467 AN: 3468

East Asian (EAS) AF: 0.587 AC: 2961 AN: 5042

South Asian (SAS) AF: 0.450 AC: 2156 AN: 4788

European-Finnish (FIN) AF: 0.330 AC: 3447 AN: 10448

Middle Eastern (MID) AF: 0.442 AC: 130 AN: 294

European-Non Finnish (NFE) AF: 0.347 AC: 23521 AN: 67790

Other (OTH) AF: 0.355 AC: 747 AN: 2102

Alfa AF: 0.362 Hom.: 27177

Bravo AF: 0.375

Asia WGS AF: 0.439 AC: 1522 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.22
DANN	Benign	0.48
PhyloP100		-0.36
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2240339; hg19: chr1-17674108;