rs1103229

chr22-21667716-G-Achr22-21667716-G-T

Variant summary

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

The NM_014337.4(PPIL2):c.32+1585G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.114 in 150,342 control chromosomes in the GnomAD database, including 1,230 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 0.11 (1230 hom., cov: 30)
• Consequence: PPIL2 NM_014337.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.333

Genes affected

PPIL2 (HGNC:9261): (peptidylprolyl isomerase like 2) This gene is a member of the cyclophilin family of peptidylprolyl isomerases. The cyclophilins are a highly conserved ubiquitous family, members of which play an important role in protein folding, immunosuppression by cyclosporin A, and infection of HIV-1 virions. This protein interacts with the proteinase inhibitor eglin c and is localized in the nucleus. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Dec 2015]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.16 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PPIL2	NM_014337.4	c.32+1585G>A		intron_variant		ENST00000398831.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PPIL2	ENST00000398831.8	c.32+1585G>A		intron_variant		1	NM_014337.4	P1

Frequencies

GnomAD3 genomes AF: 0.114 AC: 17136 AN: 150276 Hom.: 1229 Cov.: 30

Gnomad AFR AF: 0.0390

Gnomad AMI AF: 0.137

Gnomad AMR AF: 0.110

Gnomad ASJ AF: 0.138

Gnomad EAS AF: 0.000783

Gnomad SAS AF: 0.0977

Gnomad FIN AF: 0.151

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.162

Gnomad OTH AF: 0.131

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

GnomAD4 genome AF: 0.114 AC: 17139 AN: 150342 Hom.: 1230 Cov.: 30 AF XY: 0.111 AC XY: 8162 AN XY: 73234

Gnomad4 AFR AF: 0.0389

Gnomad4 AMR AF: 0.109

Gnomad4 ASJ AF: 0.138

Gnomad4 EAS AF: 0.000785

Gnomad4 SAS AF: 0.0986

Gnomad4 FIN AF: 0.151

Gnomad4 NFE AF: 0.162

Gnomad4 OTH AF: 0.129

Alfa AF: 0.152 Hom.: 2469

Bravo AF: 0.108

Asia WGS AF: 0.0420 AC: 148 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	3.4
Dann	Benign	0.25

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: rs1103229; hg19: chr22-22022005;