17-34942885-C-T
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Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2
The NM_006584.4(CCT6B):c.636G>A(p.Leu212=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000804 in 1,602,808 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00067 ( 1 hom., cov: 32)
Exomes 𝑓: 0.00082 ( 5 hom. )
Consequence
CCT6B
NM_006584.4 synonymous
NM_006584.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 2.39
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 Benign. Variant got -9 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.36).
BP6
Variant 17-34942885-C-T is Benign according to our data. Variant chr17-34942885-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 3250571.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=2.39 with no splicing effect.
BS2
High Homozygotes in GnomAdExome4 at 5 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCT6B | NM_006584.4 | c.636G>A | p.Leu212= | synonymous_variant | 6/14 | ENST00000314144.10 | |
CCT6B | NM_001193530.2 | c.501G>A | p.Leu167= | synonymous_variant | 5/13 | ||
CCT6B | NM_001193529.3 | c.615-242G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCT6B | ENST00000314144.10 | c.636G>A | p.Leu212= | synonymous_variant | 6/14 | 1 | NM_006584.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000671 AC: 102AN: 152122Hom.: 1 Cov.: 32
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GnomAD3 exomes AF: 0.00108 AC: 262AN: 243582Hom.: 1 AF XY: 0.00111 AC XY: 146AN XY: 131656
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GnomAD4 exome AF: 0.000818 AC: 1187AN: 1450570Hom.: 5 Cov.: 28 AF XY: 0.000935 AC XY: 675AN XY: 721618
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GnomAD4 genome AF: 0.000670 AC: 102AN: 152238Hom.: 1 Cov.: 32 AF XY: 0.000779 AC XY: 58AN XY: 74440
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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 | Jun 01, 2024 | CCT6B: BP4, BP7 - |
Computational scores
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Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at