Genetic Variant PADI4:c.93-2057C>T (chr1-17328912-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_012387.3(PADI4):c.93-2057C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.666 in 151,096 control chromosomes in the GnomAD database, including 33,686 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 0.67 ( 33686 hom., cov: 29)

Consequence

PADI4
NM_012387.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.372

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.99).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.694 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PADI4	NM_012387.3 link	c.93-2057C>T		intron_variant	Intron 1 of 15	ENST00000375448.4	NP_036519.2	Q9UM07

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PADI4	ENST00000375448.4 link	c.93-2057C>T		intron_variant	Intron 1 of 15	1	NM_012387.3	ENSP00000364597.4		Q9UM07
PADI4	ENST00000375453.5 link	c.93-2057C>T		intron_variant	Intron 1 of 3	2		ENSP00000364602.1		B1AQ67

Frequencies

GnomAD3 genomes

AF:

0.666

AC:

100574

AN:

150986

Hom.:

33675

Cov.:

show subpopulations

Gnomad AFR

AF:

0.629

Gnomad AMI

AF:

0.729

Gnomad AMR

AF:

0.619

Gnomad ASJ

AF:

0.691

Gnomad EAS

AF:

0.643

Gnomad SAS

AF:

0.595

Gnomad FIN

AF:

0.703

Gnomad MID

AF:

0.637

Gnomad NFE

AF:

0.699

Gnomad OTH

AF:

0.636

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

GnomAD4 genome

AF:

0.666

AC:

100625

AN:

151096

Hom.:

33686

Cov.:

AF XY:

0.665

AC XY:

49049

AN XY:

73798

show subpopulations

Gnomad4 AFR

AF:

0.630

Gnomad4 AMR

AF:

0.618

Gnomad4 ASJ

AF:

0.691

Gnomad4 EAS

AF:

0.642

Gnomad4 SAS

AF:

0.594

Gnomad4 FIN

AF:

0.703

Gnomad4 NFE

AF:

0.699

Gnomad4 OTH

AF:

0.629

Alfa

AF:

0.683

Hom.:

58591

Bravo

AF:

0.656

Asia WGS

AF:

0.577

AC:

2002

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

2.9

DANN

Benign

0.63

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over