rs1886301

Variant names:

• chr1-17308916-G-A
• rs1886301
• NM_012387.3:c.92+602G>A

Your query was ambiguous. Multiple possible variants found:

• chr1-17308916-G-A
• chr1-17308916-G-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.92+602G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.385 in 151,916 control chromosomes in the GnomAD database, including 12,027 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 0.39 (12027 hom., cov: 30)
• Consequence: PADI4 NM_012387.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.473
• Publications: 9 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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.619 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PADI4	NM_012387.3	c.92+602G>A		intron_variant	Intron 1 of 15	ENST00000375448.4	NP_036519.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PADI4	ENST00000375448.4	c.92+602G>A		intron_variant	Intron 1 of 15	1	NM_012387.3	ENSP00000364597.4
PADI4	ENST00000375453.5	c.92+602G>A		intron_variant	Intron 1 of 3	2		ENSP00000364602.1

Frequencies

GnomAD3 genomes AF: 0.386 AC: 58539 AN: 151798 Hom.: 12035 Cov.: 30

Gnomad AFR AF: 0.256

Gnomad AMI AF: 0.317

Gnomad AMR AF: 0.422

Gnomad ASJ AF: 0.508

Gnomad EAS AF: 0.637

Gnomad SAS AF: 0.465

Gnomad FIN AF: 0.433

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.418

Gnomad OTH AF: 0.383

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

GnomAD4 genome AF: 0.385 AC: 58539 AN: 151916 Hom.: 12027 Cov.: 30 AF XY: 0.388 AC XY: 28841 AN XY: 74244

African (AFR) AF: 0.255 AC: 10573 AN: 41386

American (AMR) AF: 0.422 AC: 6447 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.508 AC: 1762 AN: 3466

East Asian (EAS) AF: 0.637 AC: 3292 AN: 5170

South Asian (SAS) AF: 0.465 AC: 2233 AN: 4798

European-Finnish (FIN) AF: 0.433 AC: 4574 AN: 10562

Middle Eastern (MID) AF: 0.507 AC: 148 AN: 292

European-Non Finnish (NFE) AF: 0.418 AC: 28425 AN: 67950

Other (OTH) AF: 0.379 AC: 796 AN: 2100

Alfa AF: 0.389 Hom.: 1937

Bravo AF: 0.380

Asia WGS AF: 0.480 AC: 1668 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	7.8
DANN	Benign	0.68
PhyloP100		0.47
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: rs1886301; hg19: chr1-17635411; COSMIC: COSV64923314;