rs1748021

Variant names:

• chr1-17341775-A-G
• rs1748021
• NM_012387.3:c.653-168A>G

Your query was ambiguous. Multiple possible variants found:

• chr1-17341775-A-G
• chr1-17341775-A-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.653-168A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.682 in 152,128 control chromosomes in the GnomAD database, including 35,439 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 0.68 (35439 hom., cov: 33)
• Consequence: PADI4 NM_012387.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.358
• Publications: 8 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=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.693 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PADI4	NM_012387.3	c.653-168A>G		intron_variant	Intron 6 of 15	ENST00000375448.4	NP_036519.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PADI4	ENST00000375448.4	c.653-168A>G		intron_variant	Intron 6 of 15	1	NM_012387.3	ENSP00000364597.4

Frequencies

GnomAD3 genomes AF: 0.682 AC: 103623 AN: 152010 Hom.: 35422 Cov.: 33

Gnomad AFR AF: 0.684

Gnomad AMI AF: 0.729

Gnomad AMR AF: 0.625

Gnomad ASJ AF: 0.691

Gnomad EAS AF: 0.646

Gnomad SAS AF: 0.600

Gnomad FIN AF: 0.700

Gnomad MID AF: 0.642

Gnomad NFE AF: 0.699

Gnomad OTH AF: 0.650

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

GnomAD4 genome AF: 0.682 AC: 103687 AN: 152128 Hom.: 35439 Cov.: 33 AF XY: 0.679 AC XY: 50517 AN XY: 74362

African (AFR) AF: 0.684 AC: 28388 AN: 41484

American (AMR) AF: 0.624 AC: 9534 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.691 AC: 2400 AN: 3472

East Asian (EAS) AF: 0.646 AC: 3341 AN: 5172

South Asian (SAS) AF: 0.599 AC: 2890 AN: 4826

European-Finnish (FIN) AF: 0.700 AC: 7402 AN: 10570

Middle Eastern (MID) AF: 0.660 AC: 194 AN: 294

European-Non Finnish (NFE) AF: 0.699 AC: 47518 AN: 68004

Other (OTH) AF: 0.643 AC: 1357 AN: 2112

Alfa AF: 0.696 Hom.: 5688

Bravo AF: 0.675

Asia WGS AF: 0.589 AC: 2047 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.0
DANN	Benign	0.34
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: rs1748021; hg19: chr1-17668270; COSMIC: COSV64923558; COSMIC: COSV64923558;