chr5-123029387-TC-T
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Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_ModerateBS2
The NM_000943.5(PPIC):βc.148delβ(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 (β ). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: π 0.0049 ( 3 hom., cov: 33)
Exomes π: 0.0072 ( 53 hom. )
Consequence
PPIC
NM_000943.5 frameshift
NM_000943.5 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 4.74
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]
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]
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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 | c.148del | p.Asp50MetfsTer6 | frameshift_variant | 2/5 | ENST00000306442.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PPIC | ENST00000306442.5 | c.148del | p.Asp50MetfsTer6 | frameshift_variant | 2/5 | 1 | NM_000943.5 | P1 | |
PPIC | ENST00000415659.2 | n.248del | non_coding_transcript_exon_variant | 2/2 | 2 | ||||
SNX24 | ENST00000502387.5 | downstream_gene_variant | 5 | ||||||
SNX24 | ENST00000510914.5 | downstream_gene_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.00490 AC: 746AN: 152182Hom.: 3 Cov.: 33
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GnomAD3 exomes AF: 0.00506 AC: 1256AN: 248336Hom.: 7 AF XY: 0.00519 AC XY: 696AN XY: 134012
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GnomAD4 exome AF: 0.00722 AC: 10519AN: 1455944Hom.: 53 Cov.: 30 AF XY: 0.00700 AC XY: 5065AN XY: 723284
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GnomAD4 genome AF: 0.00490 AC: 747AN: 152300Hom.: 3 Cov.: 33 AF XY: 0.00453 AC XY: 337AN XY: 74468
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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 - |
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at