rs61756415
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
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
NM_005038.3 missense
Scores
18
Clinical Significance
Conservation
PhyloP100: -0.309
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 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_single_submitter, 1 stars.
BS2
?
High Homozygotes in GnomAd at 5 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PPID | NM_005038.3 | c.529G>A | p.Val177Ile | missense_variant | 5/10 | ENST00000307720.4 | |
PPID | XM_047415844.1 | c.523-10G>A | splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PPID | ENST00000307720.4 | c.529G>A | p.Val177Ile | missense_variant | 5/10 | 1 | NM_005038.3 | P1 | |
PPID | ENST00000512699.1 | c.45-10G>A | splice_polypyrimidine_tract_variant, intron_variant, NMD_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.00813 AC: 1237AN: 152162Hom.: 5 Cov.: 33
GnomAD3 genomes
?
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GnomAD3 exomes AF: 0.00811 AC: 2038AN: 251256Hom.: 16 AF XY: 0.00826 AC XY: 1122AN XY: 135804
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GnomAD4 exome AF: 0.00877 AC: 12772AN: 1456054Hom.: 92 Cov.: 31 AF XY: 0.00861 AC XY: 6236AN XY: 724670
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GnomAD4 genome ? AF: 0.00812 AC: 1236AN: 152280Hom.: 5 Cov.: 33 AF XY: 0.00880 AC XY: 655AN XY: 74452
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ESP6500AA
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81
ExAC
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966
Asia WGS
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Apr 10, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
DEOGEN2
Benign
T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Benign
N
MutationTaster
Benign
D
PrimateAI
Benign
T
PROVEAN
Benign
N
REVEL
Benign
Sift
Benign
T
Sift4G
Benign
T
Polyphen
B
Vest4
MVP
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at