Variant chr4-158717095-CAT-C 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_005038.3(PPID):c.437_438del(p.His146ArgfsTer8) variant causes a frameshift change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00128 in 1,614,098 control chromosomes in the GnomAD database, including 9 homozygotes. Variant has been reported in ClinVar as Likely benign (★). Variant results in nonsense mediated mRNA decay.

Frequency

Genomes: 𝑓 0.0012 ( 0 hom., cov: 33)

Exomes 𝑓: 0.0013 ( 9 hom. )

Consequence

PPID
NM_005038.3 frameshift

Scores

Not classified

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 7.67

Variant links:

Genes affected

PPID (HGNC:9257): (peptidylprolyl isomerase D) 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. This protein has been shown to possess PPIase activity and, similar to other family members, can bind to the immunosuppressant cyclosporin A. [provided by RefSeq, Jul 2008]

PPID links:

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -6 ACMG points.

BP6

Variant 4-158717095-CAT-C is Benign according to our data. Variant chr4-158717095-CAT-C is described in ClinVar as [Likely_benign]. Clinvar id is 711202.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAdExome4 at 9 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PPID	NM_005038.3 linkuse as main transcript	c.437_438del	p.His146ArgfsTer8	frameshift_variant	4/10	ENST00000307720.4
PPID	XM_047415844.1 linkuse as main transcript	c.437_438del	p.His146ArgfsTer8	frameshift_variant	4/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PPID	ENST00000307720.4 linkuse as main transcript	c.437_438del	p.His146ArgfsTer8	frameshift_variant	4/10	1	NM_005038.3	P1
PPID	ENST00000512699.1 linkuse as main transcript			upstream_gene_variant		3

Frequencies

GnomAD3 genomes

AF:

0.00120

AC:

183

AN:

152238

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000892

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000458

Gnomad ASJ

AF:

0.00548

Gnomad EAS

AF:

0.0111

Gnomad SAS

AF:

0.00186

Gnomad FIN

AF:

0.000283

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000720

Gnomad OTH

AF:

0.000478

GnomAD3 exomes

AF:

0.00159

AC:

400

AN:

251408

Hom.:

AF XY:

0.00149

AC XY:

203

AN XY:

135886

show subpopulations

Gnomad AFR exome

AF:

0.000984

Gnomad AMR exome

AF:

0.00110

Gnomad ASJ exome

AF:

0.00456

Gnomad EAS exome

AF:

0.00854

Gnomad SAS exome

AF:

0.00124

Gnomad FIN exome

AF:

0.000601

Gnomad NFE exome

AF:

0.000765

Gnomad OTH exome

AF:

0.000815

GnomAD4 exome

AF:

0.00129

AC:

1889

AN:

1461742

Hom.:

AF XY:

0.00126

AC XY:

913

AN XY:

727194

show subpopulations

Gnomad4 AFR exome

AF:

0.00108

Gnomad4 AMR exome

AF:

0.00127

Gnomad4 ASJ exome

AF:

0.00398

Gnomad4 EAS exome

AF:

0.0139

Gnomad4 SAS exome

AF:

0.00128

Gnomad4 FIN exome

AF:

0.000505

Gnomad4 NFE exome

AF:

0.000804

Gnomad4 OTH exome

AF:

0.00162

GnomAD4 genome

AF:

0.00119

AC:

182

AN:

152356

Hom.:

Cov.:

AF XY:

0.00132

AC XY:

AN XY:

74504

show subpopulations

Gnomad4 AFR

AF:

0.000890

Gnomad4 AMR

AF:

0.000457

Gnomad4 ASJ

AF:

0.00548

Gnomad4 EAS

AF:

0.0108

Gnomad4 SAS

AF:

0.00207

Gnomad4 FIN

AF:

0.000283

Gnomad4 NFE

AF:

0.000720

Gnomad4 OTH

AF:

0.000473

Alfa

AF:

0.000441

Hom.:

Bravo

AF:

0.00108

Asia WGS

AF:

0.00722

AC:

AN:

3478

EpiCase

AF:

0.000545

EpiControl

AF:

0.000534

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

Labcorp Genetics (formerly Invitae), Labcorp

Aug 23, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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