rs11892119

chr2-200871389-T-C

Variant summary

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

The NM_130906.3(PPIL3):c.*6A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.128 in 1,604,924 control chromosomes in the GnomAD database, including 16,139 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 0.19 (3711 hom., cov: 31)
  • Exomes 𝑓: 0.12 (12428 hom.)
• Consequence: PPIL3 NM_130906.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.602

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=-0.67).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.365 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PPIL3	NM_130906.3	c.*6A>G		3_prime_UTR_variant	7/7	ENST00000392283.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PPIL3	ENST00000392283.9	c.*6A>G		3_prime_UTR_variant	7/7	1	NM_130906.3	P1

Frequencies

GnomAD3 genomes AF: 0.187 AC: 28479 AN: 151984 Hom.: 3703 Cov.: 31

Gnomad AFR AF: 0.370

Gnomad AMI AF: 0.120

Gnomad AMR AF: 0.136

Gnomad ASJ AF: 0.149

Gnomad EAS AF: 0.00768

Gnomad SAS AF: 0.0507

Gnomad FIN AF: 0.101

Gnomad MID AF: 0.115

Gnomad NFE AF: 0.128

Gnomad OTH AF: 0.178

GnomAD3 exomes AF: 0.117 AC: 28925 AN: 247530 Hom.: 2540 AF XY: 0.112 AC XY: 14936 AN XY: 133796

Gnomad AFR exome AF: 0.385

Gnomad AMR exome AF: 0.0781

Gnomad ASJ exome AF: 0.132

Gnomad EAS exome AF: 0.00453

Gnomad SAS exome AF: 0.0546

Gnomad FIN exome AF: 0.107

Gnomad NFE exome AF: 0.125

Gnomad OTH exome AF: 0.118

GnomAD4 exome AF: 0.121 AC: 176302 AN: 1452822 Hom.: 12428 Cov.: 30 AF XY: 0.119 AC XY: 86081 AN XY: 722920

Gnomad4 AFR exome AF: 0.378

Gnomad4 AMR exome AF: 0.0850

Gnomad4 ASJ exome AF: 0.137

Gnomad4 EAS exome AF: 0.00250

Gnomad4 SAS exome AF: 0.0561

Gnomad4 FIN exome AF: 0.107

Gnomad4 NFE exome AF: 0.124

Gnomad4 OTH exome AF: 0.128

GnomAD4 genome AF: 0.188 AC: 28525 AN: 152102 Hom.: 3711 Cov.: 31 AF XY: 0.183 AC XY: 13578 AN XY: 74384

Gnomad4 AFR AF: 0.370

Gnomad4 AMR AF: 0.136

Gnomad4 ASJ AF: 0.149

Gnomad4 EAS AF: 0.00770

Gnomad4 SAS AF: 0.0505

Gnomad4 FIN AF: 0.101

Gnomad4 NFE AF: 0.128

Gnomad4 OTH AF: 0.176

Alfa AF: 0.158 Hom.: 1641

Bravo AF: 0.200

Asia WGS AF: 0.0630 AC: 220 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
Cadd	Benign	12
Dann	Benign	0.78

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: rs11892119; hg19: chr2-201736112;