Variant chr4-158715678-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2

The NM_005038.3(PPID):c.529G>A(p.Val177Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00871 in 1,608,334 control chromosomes in the GnomAD database, including 97 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0081 ( 5 hom., cov: 33)

Exomes 𝑓: 0.0088 ( 92 hom. )

Consequence

PPID
NM_005038.3 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.309

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0057251155).

BP6

Variant 4-158715678-C-T is Benign according to our data. Variant chr4-158715678-C-T is described in ClinVar as [Benign]. Clinvar id is 789176.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS2

High Homozygotes in GnomAd4 at 5 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PPID	NM_005038.3 link	c.529G>A	p.Val177Ile	missense_variant	5/10	ENST00000307720.4	NP_005029.1	Q08752E5KN55
PPID	XM_047415844.1 link	c.523-10G>A		intron_variant			XP_047271800.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PPID	ENST00000307720.4 link	c.529G>A	p.Val177Ile	missense_variant	5/10	1	NM_005038.3	ENSP00000303754.3		Q08752
PPID	ENST00000512699.1 link	n.43-10G>A		intron_variant		3		ENSP00000423207.1		H0Y969

Frequencies

GnomAD3 genomes

AF:

0.00813

AC:

1237

AN:

152162

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00227

Gnomad AMI

AF:

0.0132

Gnomad AMR

AF:

0.00674

Gnomad ASJ

AF:

0.0159

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00622

Gnomad FIN

AF:

0.0256

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00970

Gnomad OTH

AF:

0.00574

GnomAD3 exomes

AF:

0.00811

AC:

2038

AN:

251256

Hom.:

AF XY:

0.00826

AC XY:

1122

AN XY:

135804

show subpopulations

Gnomad AFR exome

AF:

0.00209

Gnomad AMR exome

AF:

0.00269

Gnomad ASJ exome

AF:

0.0129

Gnomad EAS exome

AF:

0.000163

Gnomad SAS exome

AF:

0.00539

Gnomad FIN exome

AF:

0.0263

Gnomad NFE exome

AF:

0.00875

Gnomad OTH exome

AF:

0.00816

GnomAD4 exome

AF:

0.00877

AC:

12772

AN:

1456054

Hom.:

Cov.:

AF XY:

0.00861

AC XY:

6236

AN XY:

724670

show subpopulations

Gnomad4 AFR exome

AF:

0.00183

Gnomad4 AMR exome

AF:

0.00304

Gnomad4 ASJ exome

AF:

0.0142

Gnomad4 EAS exome

AF:

0.000151

Gnomad4 SAS exome

AF:

0.00563

Gnomad4 FIN exome

AF:

0.0258

Gnomad4 NFE exome

AF:

0.00887

Gnomad4 OTH exome

AF:

0.00849

GnomAD4 genome

AF:

0.00812

AC:

1236

AN:

152280

Hom.:

Cov.:

AF XY:

0.00880

AC XY:

655

AN XY:

74452

show subpopulations

Gnomad4 AFR

AF:

0.00226

Gnomad4 AMR

AF:

0.00674

Gnomad4 ASJ

AF:

0.0159

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00601

Gnomad4 FIN

AF:

0.0256

Gnomad4 NFE

AF:

0.00970

Gnomad4 OTH

AF:

0.00568

Alfa

AF:

0.00818

Hom.:

Bravo

AF:

0.00625

TwinsUK

AF:

0.00647

AC:

ALSPAC

AF:

0.0104

AC:

ESP6500AA

AF:

0.00318

AC:

ESP6500EA

AF:

0.00942

AC:

ExAC

AF:

0.00796

AC:

966

Asia WGS

AF:

0.00375

AC:

AN:

3478

EpiCase

AF:

0.00894

EpiControl

AF:

0.00788

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Apr 10, 2018	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.065

BayesDel_addAF

Benign

-0.65

BayesDel_noAF

Benign

-0.69

CADD

Benign

6.2

DANN

Benign

0.79

DEOGEN2

Benign

0.013

Eigen

Benign

-1.4

Eigen_PC

Benign

-1.3

FATHMM_MKL

Benign

0.20

LIST_S2

Benign

0.75

MetaRNN

Benign

0.0057

MetaSVM

Benign

-1.1

MutationAssessor

Benign

0.46

PrimateAI

Benign

0.23

PROVEAN

Benign

-0.47

REVEL

Benign

0.026

Sift

Benign

0.44

Sift4G

Benign

0.54

Polyphen

0.0050

Vest4

0.16

MVP

0.099

MPC

0.14

ClinPred

0.0085

GERP RS

-4.3

Varity_R

0.021

gMVP

0.22

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

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