rs2295899
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_030752.3(TCP1):c.798-25C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.549 in 1,536,860 control chromosomes in the GnomAD database, including 237,041 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.48 ( 19073 hom., cov: 33)
Exomes 𝑓: 0.56 ( 217968 hom. )
Consequence
TCP1
NM_030752.3 intron
NM_030752.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.07
Genes affected
TCP1 (HGNC:11655): (t-complex 1) The protein encoded by this gene is 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. Alternate transcriptional splice variants of this gene, encoding different isoforms, have been characterized. In addition, three pseudogenes that appear to be derived from this gene have been found. [provided by RefSeq, Jun 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.572 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TCP1 | NM_030752.3 | c.798-25C>T | intron_variant | ENST00000321394.12 | |||
TCP1 | NM_001008897.2 | c.333-25C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TCP1 | ENST00000321394.12 | c.798-25C>T | intron_variant | 1 | NM_030752.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.482 AC: 73283AN: 151998Hom.: 19064 Cov.: 33
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GnomAD3 exomes AF: 0.533 AC: 104567AN: 196162Hom.: 29244 AF XY: 0.535 AC XY: 57271AN XY: 107068
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GnomAD4 exome AF: 0.556 AC: 769685AN: 1384744Hom.: 217968 Cov.: 26 AF XY: 0.554 AC XY: 379707AN XY: 685894
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GnomAD4 genome ? AF: 0.482 AC: 73298AN: 152116Hom.: 19073 Cov.: 33 AF XY: 0.480 AC XY: 35691AN XY: 74374
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
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