rs1635571

Variant names:

• chr1-17346234-C-A
• rs1635571
• NM_012387.3:c.1047+95C>A

Your query was ambiguous. Multiple possible variants found:

• chr1-17346234-C-A
• chr1-17346234-C-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_012387.3(PADI4):​c.1047+95C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000346 in 578,332 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0000035 (0 hom.)
• Consequence: PADI4 NM_012387.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.646
• Publications: 0 publications found

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

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PADI4	NM_012387.3	c.1047+95C>A		intron_variant	Intron 9 of 15	ENST00000375448.4	NP_036519.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PADI4	ENST00000375448.4	c.1047+95C>A		intron_variant	Intron 9 of 15	1	NM_012387.3	ENSP00000364597.4
PADI4	ENST00000468945.1	n.106+95C>A		intron_variant	Intron 1 of 1	2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000346 AC: 2 AN: 578332 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 308188

African (AFR) AF: 0.00 AC: 0 AN: 15054

American (AMR) AF: 0.00 AC: 0 AN: 25926

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 16406

East Asian (EAS) AF: 0.00 AC: 0 AN: 32824

South Asian (SAS) AF: 0.00 AC: 0 AN: 56654

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 47552

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2342

European-Non Finnish (NFE) AF: 0.00000569 AC: 2 AN: 351206

Other (OTH) AF: 0.00 AC: 0 AN: 30368

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.087
DANN	Benign	0.47
PhyloP100		-0.65

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1635571; hg19: chr1-17672729;