NM_016059.5:c.212-7095C>A

Variant names:

• chr6-36863749-G-T
• rs13220210
• NM_016059.5:c.212-7095C>A

Variant summary

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

The NM_016059.5(PPIL1):​c.212-7095C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.129 in 151,738 control chromosomes in the GnomAD database, including 1,416 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 0.13 (1416 hom., cov: 30)
• Consequence: PPIL1 NM_016059.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02

Genes affected

PPIL1 (HGNC:9260): (peptidylprolyl isomerase like 1) This gene is a member of the cyclophilin family of peptidylprolyl isomerases (PPIases). 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. Based on similarity to other PPIases, this protein could accelerate the folding of proteins and might catalyze the cis-trans isomerization of proline imidic peptide bonds in oligopeptides. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.259 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PPIL1	NM_016059.5	c.212-7095C>A		intron_variant	Intron 2 of 3	ENST00000373699.6	NP_057143.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PPIL1	ENST00000373699.6	c.212-7095C>A		intron_variant	Intron 2 of 3	1	NM_016059.5	ENSP00000362803.5

Frequencies

GnomAD3 genomes AF: 0.129 AC: 19567 AN: 151618 Hom.: 1411 Cov.: 30

Gnomad AFR AF: 0.172

Gnomad AMI AF: 0.0868

Gnomad AMR AF: 0.114

Gnomad ASJ AF: 0.140

Gnomad EAS AF: 0.271

Gnomad SAS AF: 0.149

Gnomad FIN AF: 0.0722

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.103

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.129 AC: 19609 AN: 151738 Hom.: 1416 Cov.: 30 AF XY: 0.129 AC XY: 9570 AN XY: 74110

Gnomad4 AFR AF: 0.173

Gnomad4 AMR AF: 0.114

Gnomad4 ASJ AF: 0.140

Gnomad4 EAS AF: 0.271

Gnomad4 SAS AF: 0.149

Gnomad4 FIN AF: 0.0722

Gnomad4 NFE AF: 0.103

Gnomad4 OTH AF: 0.120

Alfa AF: 0.0405 Hom.: 32

Bravo AF: 0.134

Asia WGS AF: 0.206 AC: 717 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.099
DANN	Benign	0.88

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: rs13220210; hg19: chr6-36831525;