rs4035022

chr2-200879629-G-A

Variant summary

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

The NM_130906.3(PPIL3):c.240+1792C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.147 in 152,144 control chromosomes in the GnomAD database, including 1,871 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 0.15 (1871 hom., cov: 32)
• Consequence: PPIL3 NM_130906.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.336

Genes affected

PPIL3 (HGNC:9262): (peptidylprolyl isomerase like 3) This gene encodes a member of the cyclophilin family. Cyclophilins catalyze the cis-trans isomerization of peptidylprolyl imide bonds in oligopeptides. They have been proposed to act either as catalysts or as molecular chaperones in protein-folding events. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.6).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.195 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PPIL3	NM_130906.3	c.240+1792C>T		intron_variant		ENST00000392283.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PPIL3	ENST00000392283.9	c.240+1792C>T		intron_variant		1	NM_130906.3	P1

Frequencies

GnomAD3 genomes AF: 0.148 AC: 22424 AN: 152026 Hom.: 1869 Cov.: 32

Gnomad AFR AF: 0.199

Gnomad AMI AF: 0.143

Gnomad AMR AF: 0.127

Gnomad ASJ AF: 0.154

Gnomad EAS AF: 0.00771

Gnomad SAS AF: 0.0526

Gnomad FIN AF: 0.102

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.145

Gnomad OTH AF: 0.148

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

GnomAD4 genome AF: 0.147 AC: 22440 AN: 152144 Hom.: 1871 Cov.: 32 AF XY: 0.143 AC XY: 10624 AN XY: 74388

Gnomad4 AFR AF: 0.199

Gnomad4 AMR AF: 0.127

Gnomad4 ASJ AF: 0.154

Gnomad4 EAS AF: 0.00773

Gnomad4 SAS AF: 0.0524

Gnomad4 FIN AF: 0.102

Gnomad4 NFE AF: 0.145

Gnomad4 OTH AF: 0.146

Alfa AF: 0.153 Hom.: 244

Bravo AF: 0.154

Asia WGS AF: 0.0500 AC: 174 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
Cadd	Benign	12
Dann	Benign	0.90

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: rs4035022; hg19: chr2-201744352;