Variant rs1748032 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_012387.3(PADI4):c.408+83C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.63 in 919,052 control chromosomes in the GnomAD database, including 183,640 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 0.63 ( 30470 hom., cov: 33)

Exomes 𝑓: 0.63 ( 153170 hom. )

Consequence

PADI4
NM_012387.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.40

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 made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.644 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PADI4	NM_012387.3 linkuse as main transcript	c.408+83C>T		intron_variant		ENST00000375448.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PADI4	ENST00000375448.4 linkuse as main transcript	c.408+83C>T		intron_variant		1	NM_012387.3	P1

Frequencies

GnomAD3 genomes

AF:

0.632

AC:

96053

AN:

152006

Hom.:

30456

Cov.:

show subpopulations

Gnomad AFR

AF:

0.617

Gnomad AMI

AF:

0.690

Gnomad AMR

AF:

0.593

Gnomad ASJ

AF:

0.651

Gnomad EAS

AF:

0.641

Gnomad SAS

AF:

0.584

Gnomad FIN

AF:

0.652

Gnomad MID

AF:

0.617

Gnomad NFE

AF:

0.649

Gnomad OTH

AF:

0.600

GnomAD4 exome

AF:

0.630

AC:

483050

AN:

766928

Hom.:

153170

AF XY:

0.629

AC XY:

255341

AN XY:

405856

show subpopulations

Gnomad4 AFR exome

AF:

0.611

Gnomad4 AMR exome

AF:

0.539

Gnomad4 ASJ exome

AF:

0.639

Gnomad4 EAS exome

AF:

0.642

Gnomad4 SAS exome

AF:

0.572

Gnomad4 FIN exome

AF:

0.644

Gnomad4 NFE exome

AF:

0.645

Gnomad4 OTH exome

AF:

0.624

GnomAD4 genome

AF:

0.632

AC:

96109

AN:

152124

Hom.:

30470

Cov.:

AF XY:

0.633

AC XY:

47044

AN XY:

74362

show subpopulations

Gnomad4 AFR

AF:

0.617

Gnomad4 AMR

AF:

0.593

Gnomad4 ASJ

AF:

0.651

Gnomad4 EAS

AF:

0.641

Gnomad4 SAS

AF:

0.582

Gnomad4 FIN

AF:

0.652

Gnomad4 NFE

AF:

0.649

Gnomad4 OTH

AF:

0.592

Alfa

AF:

0.641

Hom.:

3922

Bravo

AF:

0.624

Asia WGS

AF:

0.569

AC:

1978

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.018

DANN

Benign

0.84

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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