chr1-17338318-T-G

Position:

• chr1-17338318-T-G

Variant summary

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

The NM_012387.3(PADI4):​c.526+163T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.643 in 151,968 control chromosomes in the GnomAD database, including 31,594 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 0.64 (31594 hom., cov: 32)
• Consequence: PADI4 NM_012387.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.505

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.668 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PADI4	NM_012387.3	c.526+163T>G		intron_variant		ENST00000375448.4	NP_036519.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PADI4	ENST00000375448.4	c.526+163T>G		intron_variant		1	NM_012387.3	ENSP00000364597.4

Frequencies

GnomAD3 genomes AF: 0.644 AC: 97727 AN: 151848 Hom.: 31582 Cov.: 32

Gnomad AFR AF: 0.605

Gnomad AMI AF: 0.702

Gnomad AMR AF: 0.601

Gnomad ASJ AF: 0.671

Gnomad EAS AF: 0.642

Gnomad SAS AF: 0.586

Gnomad FIN AF: 0.686

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.674

Gnomad OTH AF: 0.607

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

GnomAD4 genome AF: 0.643 AC: 97781 AN: 151968 Hom.: 31594 Cov.: 32 AF XY: 0.643 AC XY: 47767 AN XY: 74256

Gnomad4 AFR AF: 0.605

Gnomad4 AMR AF: 0.600

Gnomad4 ASJ AF: 0.671

Gnomad4 EAS AF: 0.642

Gnomad4 SAS AF: 0.585

Gnomad4 FIN AF: 0.686

Gnomad4 NFE AF: 0.674

Gnomad4 OTH AF: 0.600

Alfa AF: 0.512 Hom.: 1194

Bravo AF: 0.633

Asia WGS AF: 0.568 AC: 1976 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.8
DANN	Benign	0.73

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: rs1635585; hg19: chr1-17664813; COSMIC: COSV64923533; COSMIC: COSV64923533;