1-17354929-A-G

Variant names:

• chr1-17354929-A-G
• rs4920600
• NM_012387.3:c.1310+242A>G

Variant summary

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

The NM_012387.3(PADI4):​c.1310+242A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.763 in 152,190 control chromosomes in the GnomAD database, including 45,406 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 0.76 (45406 hom., cov: 33)
• Consequence: PADI4 NM_012387.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.129
• 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.93 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.1310+242A>G		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.1310+242A>G		intron	N/A	ENSP00000364597.4
	PADI4	ENST00000467001.1	TSL:5	n.211+242A>G		intron	N/A
	PADI4	ENST00000487048.5	TSL:3	n.277+242A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.763 AC: 116009 AN: 152072 Hom.: 45354 Cov.: 33

Gnomad AFR AF: 0.938

Gnomad AMI AF: 0.763

Gnomad AMR AF: 0.706

Gnomad ASJ AF: 0.824

Gnomad EAS AF: 0.765

Gnomad SAS AF: 0.711

Gnomad FIN AF: 0.604

Gnomad MID AF: 0.870

Gnomad NFE AF: 0.692

Gnomad OTH AF: 0.797

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

GnomAD4 genome AF: 0.763 AC: 116113 AN: 152190 Hom.: 45406 Cov.: 33 AF XY: 0.755 AC XY: 56149 AN XY: 74392

African (AFR) AF: 0.938 AC: 38984 AN: 41556

American (AMR) AF: 0.706 AC: 10791 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.824 AC: 2859 AN: 3470

East Asian (EAS) AF: 0.765 AC: 3964 AN: 5180

South Asian (SAS) AF: 0.709 AC: 3420 AN: 4826

European-Finnish (FIN) AF: 0.604 AC: 6388 AN: 10568

Middle Eastern (MID) AF: 0.874 AC: 257 AN: 294

European-Non Finnish (NFE) AF: 0.692 AC: 47073 AN: 67990

Other (OTH) AF: 0.797 AC: 1684 AN: 2114

Alfa AF: 0.734 Hom.: 11700

Bravo AF: 0.781

Asia WGS AF: 0.742 AC: 2577 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	5.2
DANN	Benign	0.46
PhyloP100		-0.13
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: rs4920600; hg19: chr1-17681424; COSMIC: COSV64923592;