rs587777929
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 1P and 4B. PP5BS2
The NM_006429.4(CCT7):c.1574C>T(p.Ser525Leu) variant causes a missense change. The variant allele was found at a frequency of 0.0000173 in 1,614,020 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Pathogenic (no stars).
Frequency
Genomes: 𝑓 0.000046 ( 0 hom., cov: 31)
Exomes 𝑓: 0.000014 ( 0 hom. )
Consequence
CCT7
NM_006429.4 missense
NM_006429.4 missense
Scores
1
14
2
Clinical Significance
Conservation
PhyloP100: 4.79
Genes affected
CCT7 (HGNC:1622): (chaperonin containing TCP1 subunit 7) This gene encodes a molecular chaperone that is a member of the chaperonin containing TCP1 complex (CCT), also known as the TCP1 ring complex (TRiC). This complex consists of two identical stacked rings, each containing eight different proteins. Unfolded polypeptides enter the central cavity of the complex and are folded in an ATP-dependent manner. The complex folds various proteins, including actin and tubulin. Alternative splicing results in multiple transcript variants. Related pseudogenes have been identified on chromosomes 5 and 6. [provided by RefSeq, Oct 2009]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -3 ACMG points.
PP5
?
Variant 2-73252803-C-T is Pathogenic according to our data. Variant chr2-73252803-C-T is described in ClinVar as [Pathogenic]. Clinvar id is 65429.Status of the report is no_assertion_criteria_provided, 0 stars.
BS2
?
High AC in GnomAd at 7 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCT7 | NM_006429.4 | c.1574C>T | p.Ser525Leu | missense_variant | 12/12 | ENST00000258091.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCT7 | ENST00000258091.10 | c.1574C>T | p.Ser525Leu | missense_variant | 12/12 | 1 | NM_006429.4 | P1 | |
CCT7 | ENST00000539919.5 | c.1442C>T | p.Ser481Leu | missense_variant | 13/13 | 2 | |||
CCT7 | ENST00000540468.5 | c.1313C>T | p.Ser438Leu | missense_variant | 10/10 | 2 | |||
CCT7 | ENST00000398422.2 | c.962C>T | p.Ser321Leu | missense_variant | 7/7 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000460 AC: 7AN: 152156Hom.: 0 Cov.: 31
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?
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GnomAD3 exomes AF: 0.0000200 AC: 5AN: 249452Hom.: 0 AF XY: 0.0000369 AC XY: 5AN XY: 135372
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GnomAD4 exome AF: 0.0000144 AC: 21AN: 1461864Hom.: 0 Cov.: 31 AF XY: 0.0000206 AC XY: 15AN XY: 727230
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GnomAD4 genome ? AF: 0.0000460 AC: 7AN: 152156Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74344
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ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Myocardial infarction 1 Pathogenic:1
Pathogenic, no assertion criteria provided | research | Institut für Integrative und Experimentelle Genomik, Universität zu Lübeck | Sep 15, 2013 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Uncertain
D
BayesDel_noAF
Uncertain
Cadd
Uncertain
Dann
Uncertain
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;D;D;D
M_CAP
Uncertain
D
MetaRNN
Uncertain
D;D;D;D
MetaSVM
Uncertain
T
MutationTaster
Benign
D;D;D;D;D;D;D
PrimateAI
Uncertain
T
PROVEAN
Uncertain
D;D;D;D
REVEL
Pathogenic
Sift
Uncertain
D;D;D;D
Sift4G
Uncertain
D;D;D;D
Polyphen
0.93
.;.;P;.
Vest4
MutPred
0.34
.;.;Gain of catalytic residue at S525 (P = 0.0025);.;
MVP
MPC
0.45
ClinPred
D
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
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