NM_012387.3:c.1558+378T>C

Variant names:

• chr1-17356837-T-C
• rs1635565
• NM_012387.3:c.1558+378T>C

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_012387.3(PADI4):​c.1558+378T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 (37313 hom., cov: 26)
  • Failed GnomAD Quality Control
• Consequence: PADI4 NM_012387.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.384
• Publications: 3 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: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PADI4	NM_012387.3	MANE Select	c.1558+378T>C		intron	N/A	NP_036519.2	Q9UM07

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PADI4	ENST00000375448.4	TSL:1 MANE Select	c.1558+378T>C		intron	N/A	ENSP00000364597.4	Q9UM07
	PADI4	ENST00000467001.1	TSL:5	n.459+378T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.732 AC: 105517 AN: 144098 Hom.: 37288 Cov.: 26

Gnomad AFR AF: 0.755

Gnomad AMI AF: 0.785

Gnomad AMR AF: 0.694

Gnomad ASJ AF: 0.841

Gnomad EAS AF: 0.787

Gnomad SAS AF: 0.702

Gnomad FIN AF: 0.687

Gnomad MID AF: 0.774

Gnomad NFE AF: 0.724

Gnomad OTH AF: 0.751

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

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.732 AC: 105585 AN: 144200 Hom.: 37313 Cov.: 26 AF XY: 0.728 AC XY: 51033 AN XY: 70084

African (AFR) AF: 0.755 AC: 29740 AN: 39400

American (AMR) AF: 0.694 AC: 9812 AN: 14140

Ashkenazi Jewish (ASJ) AF: 0.841 AC: 2882 AN: 3426

East Asian (EAS) AF: 0.788 AC: 3837 AN: 4870

South Asian (SAS) AF: 0.701 AC: 3104 AN: 4426

European-Finnish (FIN) AF: 0.687 AC: 6596 AN: 9604

Middle Eastern (MID) AF: 0.779 AC: 226 AN: 290

European-Non Finnish (NFE) AF: 0.724 AC: 47188 AN: 65150

Other (OTH) AF: 0.749 AC: 1512 AN: 2018

Alfa AF: 0.646 Hom.: 1915

Bravo AF: 0.707

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.19
DANN	Benign	0.26
PhyloP100		-0.38
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: rs1635565; hg19: chr1-17683332; COSMIC: COSV64923615; COSMIC: COSV64923615;