chr1-17358679-T-C

Position:

• chr1-17358679-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_012387.3(PADI4):​c.1559-159T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.744 in 151,592 control chromosomes in the GnomAD database, including 42,654 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 0.74 (42654 hom., cov: 31)
• Consequence: PADI4 NM_012387.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.172

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.862 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PADI4	NM_012387.3	c.1559-159T>C		intron_variant		ENST00000375448.4	NP_036519.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PADI4	ENST00000375448.4	c.1559-159T>C		intron_variant		1	NM_012387.3	ENSP00000364597.4
PADI4	ENST00000467001.1	n.460-159T>C		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.744 AC: 112696 AN: 151476 Hom.: 42609 Cov.: 31

Gnomad AFR AF: 0.870

Gnomad AMI AF: 0.759

Gnomad AMR AF: 0.673

Gnomad ASJ AF: 0.834

Gnomad EAS AF: 0.792

Gnomad SAS AF: 0.655

Gnomad FIN AF: 0.636

Gnomad MID AF: 0.783

Gnomad NFE AF: 0.698

Gnomad OTH AF: 0.758

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

GnomAD4 genome AF: 0.744 AC: 112792 AN: 151592 Hom.: 42654 Cov.: 31 AF XY: 0.736 AC XY: 54564 AN XY: 74098

Gnomad4 AFR AF: 0.870

Gnomad4 AMR AF: 0.673

Gnomad4 ASJ AF: 0.834

Gnomad4 EAS AF: 0.793

Gnomad4 SAS AF: 0.654

Gnomad4 FIN AF: 0.636

Gnomad4 NFE AF: 0.698

Gnomad4 OTH AF: 0.755

Alfa AF: 0.710 Hom.: 17291

Bravo AF: 0.755

Asia WGS AF: 0.725 AC: 2520 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	3.2
DANN	Benign	0.53

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

Other links and lift over

dbSNP: rs2428735; hg19: chr1-17685174; COSMIC: COSV64923633; COSMIC: COSV64923633;