1-17352218-T-C

Position:

• chr1-17352218-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.1156-2315T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0185 in 90,158 control chromosomes in the GnomAD database, including 26 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 0.019 (26 hom., cov: 23)
• Consequence: PADI4 NM_012387.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.57

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=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.052 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PADI4	NM_012387.3	c.1156-2315T>C		intron_variant		ENST00000375448.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PADI4	ENST00000375448.4	c.1156-2315T>C		intron_variant		1	NM_012387.3	P1
PADI4	ENST00000467001.1	n.57-2315T>C		intron_variant, non_coding_transcript_variant		5
PADI4	ENST00000487048.5	n.123-2315T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.0185 AC: 1666 AN: 90102 Hom.: 27 Cov.: 23

Gnomad AFR AF: 0.0548

Gnomad AMI AF: 0.0217

Gnomad AMR AF: 0.00759

Gnomad ASJ AF: 0.0109

Gnomad EAS AF: 0.00917

Gnomad SAS AF: 0.00671

Gnomad FIN AF: 0.00329

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.00974

Gnomad OTH AF: 0.0193

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

GnomAD4 genome AF: 0.0185 AC: 1668 AN: 90158 Hom.: 26 Cov.: 23 AF XY: 0.0195 AC XY: 857 AN XY: 43990

Gnomad4 AFR AF: 0.0548

Gnomad4 AMR AF: 0.00758

Gnomad4 ASJ AF: 0.0109

Gnomad4 EAS AF: 0.00917

Gnomad4 SAS AF: 0.00672

Gnomad4 FIN AF: 0.00329

Gnomad4 NFE AF: 0.00974

Gnomad4 OTH AF: 0.0191

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.054
DANN	Benign	0.15

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: rs12042956; hg19: chr1-17678713;