rs1748011

Variant names:

• chr1-17356786-C-A
• rs1748011
• NM_012387.3:c.1558+327C>A

Your query was ambiguous. Multiple possible variants found:

• chr1-17356786-C-A
• chr1-17356786-C-G
• chr1-17356786-C-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.1558+327C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.734 in 149,242 control chromosomes in the GnomAD database, including 40,084 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 0.73 (40084 hom., cov: 28)
• Consequence: PADI4 NM_012387.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.00
• Publications: 4 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 (AFR) allele frequency at 95% confidence interval = 0.802 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.1558+327C>A		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.1558+327C>A		intron	N/A	ENSP00000364597.4
	PADI4	ENST00000467001.1	TSL:5	n.459+327C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.734 AC: 109499 AN: 149142 Hom.: 40042 Cov.: 28

Gnomad AFR AF: 0.809

Gnomad AMI AF: 0.762

Gnomad AMR AF: 0.692

Gnomad ASJ AF: 0.834

Gnomad EAS AF: 0.794

Gnomad SAS AF: 0.668

Gnomad FIN AF: 0.671

Gnomad MID AF: 0.780

Gnomad NFE AF: 0.701

Gnomad OTH AF: 0.750

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

GnomAD4 genome AF: 0.734 AC: 109594 AN: 149242 Hom.: 40084 Cov.: 28 AF XY: 0.732 AC XY: 53064 AN XY: 72522

African (AFR) AF: 0.810 AC: 33042 AN: 40806

American (AMR) AF: 0.692 AC: 10044 AN: 14518

Ashkenazi Jewish (ASJ) AF: 0.834 AC: 2890 AN: 3464

East Asian (EAS) AF: 0.795 AC: 4005 AN: 5038

South Asian (SAS) AF: 0.668 AC: 3120 AN: 4670

European-Finnish (FIN) AF: 0.671 AC: 6702 AN: 9994

Middle Eastern (MID) AF: 0.782 AC: 230 AN: 294

European-Non Finnish (NFE) AF: 0.701 AC: 47324 AN: 67484

Other (OTH) AF: 0.748 AC: 1550 AN: 2072

Alfa AF: 0.696 Hom.: 10295

Bravo AF: 0.732

Asia WGS AF: 0.723 AC: 2513 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.049
DANN	Benign	0.78
PhyloP100		-2.0
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: rs1748011; hg19: chr1-17683281; COSMIC: COSV64923607; COSMIC: COSV64923607;