rs10788656

Positions:

• chr1-17110835-G-C

Variant summary

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

The NM_007365.3(PADI2):​c.93-5774C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.606 in 151,926 control chromosomes in the GnomAD database, including 29,976 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 0.61 (29976 hom., cov: 33)
• Consequence: PADI2 NM_007365.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.39

Genes affected

PADI2 (HGNC:18341): (peptidyl arginine deiminase 2) This gene encodes a member of the peptidyl arginine deiminase family of enzymes, which catalyze the post-translational deimination of proteins by converting arginine residues into citrullines in the presence of calcium ions. The family members have distinct substrate specificities and tissue-specific expression patterns. The type II enzyme is the most widely expressed family member. Known substrates for this enzyme include myelin basic protein in the central nervous system and vimentin in skeletal muscle and macrophages. This enzyme is thought to play a role in the onset and progression of neurodegenerative human disorders, including Alzheimer disease and multiple sclerosis, and it has also been implicated in glaucoma pathogenesis. This gene exists in a cluster with four other paralogous genes. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.85 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PADI2	NM_007365.3	c.93-5774C>G		intron_variant		ENST00000375486.9	NP_031391.2
PADI2	XM_047442975.1	c.93-5774C>G		intron_variant			XP_047298931.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PADI2	ENST00000375486.9	c.93-5774C>G		intron_variant		1	NM_007365.3	ENSP00000364635	P1
PADI2	ENST00000375481.1	c.93-5774C>G		intron_variant		1		ENSP00000364630

Frequencies

GnomAD3 genomes AF: 0.606 AC: 91985 AN: 151808 Hom.: 29966 Cov.: 33

Gnomad AFR AF: 0.350

Gnomad AMI AF: 0.754

Gnomad AMR AF: 0.660

Gnomad ASJ AF: 0.550

Gnomad EAS AF: 0.871

Gnomad SAS AF: 0.750

Gnomad FIN AF: 0.735

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.699

Gnomad OTH AF: 0.607

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

GnomAD4 genome AF: 0.606 AC: 92013 AN: 151926 Hom.: 29976 Cov.: 33 AF XY: 0.610 AC XY: 45285 AN XY: 74242

Gnomad4 AFR AF: 0.350

Gnomad4 AMR AF: 0.661

Gnomad4 ASJ AF: 0.550

Gnomad4 EAS AF: 0.871

Gnomad4 SAS AF: 0.750

Gnomad4 FIN AF: 0.735

Gnomad4 NFE AF: 0.699

Gnomad4 OTH AF: 0.608

Alfa AF: 0.647 Hom.: 4161

Bravo AF: 0.586

Asia WGS AF: 0.744 AC: 2587 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	7.6
DANN	Benign	0.65

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: rs10788656; hg19: chr1-17437330; COSMIC: COSV64945558;