chr17-34954439-T-A
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Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_006584.4(CCT6B):c.497A>T(p.Asp166Val) variant causes a missense change. The variant allele was found at a frequency of 0.00000561 in 1,605,388 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000033 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0000028 ( 0 hom. )
Consequence
CCT6B
NM_006584.4 missense
NM_006584.4 missense
Scores
5
10
3
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 4.68
Genes affected
CCT6B (HGNC:1621): (chaperonin containing TCP1 subunit 6B) 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. [provided by RefSeq, Feb 2015]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PP3
MetaRNN computational evidence supports a deleterious effect, 0.81
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCT6B | NM_006584.4 | c.497A>T | p.Asp166Val | missense_variant | 4/14 | ENST00000314144.10 | |
CCT6B | NM_001193529.3 | c.497A>T | p.Asp166Val | missense_variant | 4/13 | ||
CCT6B | NM_001193530.2 | c.362A>T | p.Asp121Val | missense_variant | 3/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCT6B | ENST00000314144.10 | c.497A>T | p.Asp166Val | missense_variant | 4/14 | 1 | NM_006584.4 | P1 | |
CCT6B | ENST00000421975.7 | c.497A>T | p.Asp166Val | missense_variant | 4/13 | 1 | |||
CCT6B | ENST00000436961.7 | c.362A>T | p.Asp121Val | missense_variant | 3/13 | 2 | |||
CCT6B | ENST00000585073.1 | c.71A>T | p.Asp24Val | missense_variant | 2/5 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000328 AC: 5AN: 152238Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.00000413 AC: 1AN: 241968Hom.: 0 AF XY: 0.00000763 AC XY: 1AN XY: 131076
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GnomAD4 exome AF: 0.00000275 AC: 4AN: 1453150Hom.: 0 Cov.: 30 AF XY: 0.00000415 AC XY: 3AN XY: 722702
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GnomAD4 genome AF: 0.0000328 AC: 5AN: 152238Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74368
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Uncertain
D
BayesDel_noAF
Uncertain
CADD
Benign
DANN
Uncertain
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Pathogenic
D;D;D;D
M_CAP
Uncertain
D
MetaRNN
Pathogenic
D;D;D;D
MetaSVM
Uncertain
D
MutationAssessor
Pathogenic
M;M;.;.
MutationTaster
Benign
D;D;D
PrimateAI
Benign
T
PROVEAN
Pathogenic
D;D;D;.
REVEL
Pathogenic
Sift
Uncertain
D;D;D;.
Sift4G
Uncertain
D;D;D;D
Polyphen
0.35
.;B;.;.
Vest4
MutPred
Loss of helix (P = 0.0104);Loss of helix (P = 0.0104);.;.;
MVP
MPC
0.26
ClinPred
D
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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