dbSNP rs12746451: PADI4:c.1155+278C>T (chr1-17348326-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_012387.3(PADI4):c.1155+278C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0841 in 283,278 control chromosomes in the GnomAD database, including 1,243 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 0.091 ( 808 hom., cov: 33)

Exomes 𝑓: 0.076 ( 435 hom. )

Consequence

PADI4
NM_012387.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.995

Publications

6 publications found

Variant links:

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]

PADI4 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.159 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PADI4	NM_012387.3	MANE Select	c.1155+278C>T		intron	N/A	NP_036519.2	Q9UM07

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
PADI4	ENST00000375448.4	TSL:1 MANE Select	c.1155+278C>T	intron	N/A	ENSP00000364597.4	Q9UM07
PADI4	ENST00000487048.5	TSL:3	n.122+278C>T	intron	N/A
PADI4	ENST00000468945.1	TSL:2	n.*119C>T	downstream_gene	N/A

Frequencies

GnomAD3 genomes

AF:

0.0906

AC:

13779

AN:

152128

Hom.:

804

Cov.:

show subpopulations

Gnomad AFR

AF:

0.161

Gnomad AMI

AF:

0.0319

Gnomad AMR

AF:

0.0593

Gnomad ASJ

AF:

0.0487

Gnomad EAS

AF:

0.0488

Gnomad SAS

AF:

0.0318

Gnomad FIN

AF:

0.0714

Gnomad MID

AF:

0.0601

Gnomad NFE

AF:

0.0679

Gnomad OTH

AF:

0.0876

GnomAD4 exome

AF:

0.0764

AC:

10010

AN:

131032

Hom.:

435

AF XY:

0.0752

AC XY:

5082

AN XY:

67596

show subpopulations

African (AFR)

AF:

0.185

AC:

912

AN:

4942

American (AMR)

AF:

0.0514

AC:

270

AN:

5254

Ashkenazi Jewish (ASJ)

AF:

0.0539

AC:

257

AN:

4766

East Asian (EAS)

AF:

0.0599

AC:

521

AN:

8698

South Asian (SAS)

AF:

0.0458

AC:

343

AN:

7496

European-Finnish (FIN)

AF:

0.0748

AC:

580

AN:

7754

Middle Eastern (MID)

AF:

0.0817

AC:

AN:

612

European-Non Finnish (NFE)

AF:

0.0769

AC:

6392

AN:

83172

Other (OTH)

AF:

0.0822

AC:

685

AN:

8338

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.517

Heterozygous variant carriers

455

911

1366

1822

2277

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

126

168

210

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0907

AC:

13815

AN:

152246

Hom.:

808

Cov.:

AF XY:

0.0890

AC XY:

6622

AN XY:

74444

show subpopulations

African (AFR)

AF:

0.162

AC:

6721

AN:

41522

American (AMR)

AF:

0.0592

AC:

906

AN:

15306

Ashkenazi Jewish (ASJ)

AF:

0.0487

AC:

169

AN:

3468

East Asian (EAS)

AF:

0.0485

AC:

251

AN:

5176

South Asian (SAS)

AF:

0.0319

AC:

154

AN:

4834

European-Finnish (FIN)

AF:

0.0714

AC:

758

AN:

10612

Middle Eastern (MID)

AF:

0.0680

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0680

AC:

4622

AN:

68012

Other (OTH)

AF:

0.0876

AC:

185

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

635

1270

1904

2539

3174

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

144

288

432

576

720

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0732

Hom.:

652

Bravo

AF:

0.0923

Asia WGS

AF:

0.0780

AC:

271

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

0.20

(source)

DANN

Benign

0.81

PhyloP100

-0.99

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over