rs4920600

chr1-17354929-A-Gchr1-17354929-A-T

Variant summary

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

The NM_012387.3(PADI4):c.1310+242A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.763 in 152,190 control chromosomes in the GnomAD database, including 45,406 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 0.76 (45406 hom., cov: 33)
• Consequence: PADI4 NM_012387.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.129

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 (AFR) allele frequency at 95% confidence interval = 0.93 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PADI4	NM_012387.3	c.1310+242A>G		intron_variant		ENST00000375448.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PADI4	ENST00000375448.4	c.1310+242A>G		intron_variant		1	NM_012387.3	P1
PADI4	ENST00000467001.1	n.211+242A>G		intron_variant, non_coding_transcript_variant		5
PADI4	ENST00000487048.5	n.277+242A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.763 AC: 116009 AN: 152072 Hom.: 45354 Cov.: 33

Gnomad AFR AF: 0.938

Gnomad AMI AF: 0.763

Gnomad AMR AF: 0.706

Gnomad ASJ AF: 0.824

Gnomad EAS AF: 0.765

Gnomad SAS AF: 0.711

Gnomad FIN AF: 0.604

Gnomad MID AF: 0.870

Gnomad NFE AF: 0.692

Gnomad OTH AF: 0.797

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

GnomAD4 genome AF: 0.763 AC: 116113 AN: 152190 Hom.: 45406 Cov.: 33 AF XY: 0.755 AC XY: 56149 AN XY: 74392

Gnomad4 AFR AF: 0.938

Gnomad4 AMR AF: 0.706

Gnomad4 ASJ AF: 0.824

Gnomad4 EAS AF: 0.765

Gnomad4 SAS AF: 0.709

Gnomad4 FIN AF: 0.604

Gnomad4 NFE AF: 0.692

Gnomad4 OTH AF: 0.797

Alfa AF: 0.721 Hom.: 4703

Bravo AF: 0.781

Asia WGS AF: 0.742 AC: 2577 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	5.2
Dann	Benign	0.46

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: rs4920600; hg19: chr1-17681424; COSMIC: COSV64923592;