Variant 5-123029387-TC-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_ModerateBS2

The NM_000943.5(PPIC):c.148del(p.Asp50MetfsTer6) variant causes a frameshift change. The variant allele was found at a frequency of 0.00701 in 1,608,244 control chromosomes in the GnomAD database, including 56 homozygotes. Variant has been reported in ClinVar as Likely benign (★). Variant results in nonsense mediated mRNA decay.

Frequency

Genomes: 𝑓 0.0049 ( 3 hom., cov: 33)

Exomes 𝑓: 0.0072 ( 53 hom. )

Consequence

PPIC
NM_000943.5 frameshift

Scores

Not classified

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 4.74

Variant links:

Genes affected

PPIC (HGNC:9256): (peptidylprolyl isomerase C) The protein encoded by this gene is a member of the peptidyl-prolyl cis-trans isomerase (PPIase)) family. PPIases catalyze the cis-trans isomerization of proline imidic peptide bonds in oligopeptides and accelerate the folding of proteins. Similar to other PPIases, this protein can bind immunosuppressant cyclosporin A. [provided by RefSeq, Jul 2008]

PPIC links:

SNX24 (HGNC:21533): (sorting nexin 24) Predicted to enable phosphatidylinositol phosphate binding activity. Predicted to be involved in protein transport. Predicted to be located in cytoplasmic vesicle membrane. [provided by Alliance of Genome Resources, Apr 2022]

SNX24 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -6 ACMG points.

BP6

Variant 5-123029387-TC-T is Benign according to our data. Variant chr5-123029387-TC-T is described in ClinVar as [Likely_benign]. Clinvar id is 2655658.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAd4 at 3 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PPIC	NM_000943.5 linkuse as main transcript	c.148del	p.Asp50MetfsTer6	frameshift_variant	2/5	ENST00000306442.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris
PPIC	ENST00000306442.5 linkuse as main transcript	c.148del	p.Asp50MetfsTer6	frameshift_variant	2/5	1	NM_000943.5	P1
PPIC	ENST00000415659.2 linkuse as main transcript	n.248del		non_coding_transcript_exon_variant	2/2	2
SNX24	ENST00000502387.5 linkuse as main transcript			downstream_gene_variant		5
SNX24	ENST00000510914.5 linkuse as main transcript			downstream_gene_variant		3

Frequencies

GnomAD3 genomes

AF:

0.00490

AC:

746

AN:

152182

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00135

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00713

Gnomad ASJ

AF:

0.0133

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.00228

Gnomad FIN

AF:

0.000188

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.00730

Gnomad OTH

AF:

0.0105

GnomAD3 exomes

AF:

0.00506

AC:

1256

AN:

248336

Hom.:

AF XY:

0.00519

AC XY:

696

AN XY:

134012

show subpopulations

Gnomad AFR exome

AF:

0.000925

Gnomad AMR exome

AF:

0.00444

Gnomad ASJ exome

AF:

0.0135

Gnomad EAS exome

AF:

0.000109

Gnomad SAS exome

AF:

0.00187

Gnomad FIN exome

AF:

0.000742

Gnomad NFE exome

AF:

0.00739

Gnomad OTH exome

AF:

0.00806

GnomAD4 exome

AF:

0.00722

AC:

10519

AN:

1455944

Hom.:

Cov.:

AF XY:

0.00700

AC XY:

5065

AN XY:

723284

show subpopulations

Gnomad4 AFR exome

AF:

0.00102

Gnomad4 AMR exome

AF:

0.00488

Gnomad4 ASJ exome

AF:

0.0121

Gnomad4 EAS exome

AF:

0.0000505

Gnomad4 SAS exome

AF:

0.00220

Gnomad4 FIN exome

AF:

0.000619

Gnomad4 NFE exome

AF:

0.00830

Gnomad4 OTH exome

AF:

0.00805

GnomAD4 genome

AF:

0.00490

AC:

747

AN:

152300

Hom.:

Cov.:

AF XY:

0.00453

AC XY:

337

AN XY:

74468

show subpopulations

Gnomad4 AFR

AF:

0.00135

Gnomad4 AMR

AF:

0.00713

Gnomad4 ASJ

AF:

0.0133

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.00249

Gnomad4 FIN

AF:

0.000188

Gnomad4 NFE

AF:

0.00731

Gnomad4 OTH

AF:

0.0104

Alfa

AF:

0.00223

Hom.:

Bravo

AF:

0.00527

Asia WGS

AF:

0.00115

AC:

AN:

3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Mar 01, 2023

PPIC: BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over