chr1-17336046-A-C

Variant names:

• chr1-17336046-A-C
• rs1748034
• NM_012387.3:c.341-113A>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_012387.3(PADI4):​c.341-113A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.644 in 689,166 control chromosomes in the GnomAD database, including 144,211 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 0.65 (32174 hom., cov: 33)
  • Exomes 𝑓: 0.64 (112037 hom.)
• Consequence: PADI4 NM_012387.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.754
• Publications: 10 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 (NFE) allele frequency at 95% confidence interval = 0.67 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.341-113A>C		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.341-113A>C		intron	N/A	ENSP00000364597.4

Frequencies

GnomAD3 genomes AF: 0.649 AC: 98638 AN: 151990 Hom.: 32163 Cov.: 33

Gnomad AFR AF: 0.621

Gnomad AMI AF: 0.701

Gnomad AMR AF: 0.603

Gnomad ASJ AF: 0.672

Gnomad EAS AF: 0.641

Gnomad SAS AF: 0.586

Gnomad FIN AF: 0.686

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.675

Gnomad OTH AF: 0.613

GnomAD4 exome AF: 0.643 AC: 345295 AN: 537058 Hom.: 112037 AF XY: 0.640 AC XY: 182907 AN XY: 285660

African (AFR) AF: 0.608 AC: 9166 AN: 15066

American (AMR) AF: 0.540 AC: 15199 AN: 28130

Ashkenazi Jewish (ASJ) AF: 0.654 AC: 10892 AN: 16662

East Asian (EAS) AF: 0.641 AC: 20303 AN: 31692

South Asian (SAS) AF: 0.568 AC: 31886 AN: 56160

European-Finnish (FIN) AF: 0.674 AC: 31356 AN: 46524

Middle Eastern (MID) AF: 0.584 AC: 1439 AN: 2462

European-Non Finnish (NFE) AF: 0.664 AC: 206558 AN: 311272

Other (OTH) AF: 0.636 AC: 18496 AN: 29090

GnomAD4 genome AF: 0.649 AC: 98690 AN: 152108 Hom.: 32174 Cov.: 33 AF XY: 0.648 AC XY: 48211 AN XY: 74366

African (AFR) AF: 0.621 AC: 25766 AN: 41496

American (AMR) AF: 0.602 AC: 9206 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.672 AC: 2332 AN: 3472

East Asian (EAS) AF: 0.641 AC: 3306 AN: 5158

South Asian (SAS) AF: 0.585 AC: 2819 AN: 4820

European-Finnish (FIN) AF: 0.686 AC: 7271 AN: 10598

Middle Eastern (MID) AF: 0.633 AC: 186 AN: 294

European-Non Finnish (NFE) AF: 0.675 AC: 45886 AN: 67960

Other (OTH) AF: 0.605 AC: 1280 AN: 2114

Alfa AF: 0.593 Hom.: 2111

Bravo AF: 0.639

Asia WGS AF: 0.569 AC: 1977 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	3.2
DANN	Benign	0.46
PhyloP100		-0.75
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs1748034; hg19: chr1-17662541; COSMIC: COSV64925394; COSMIC: COSV64925394;