rs1547093
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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.489-112G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.79 in 1,030,764 control chromosomes in the GnomAD database, including 323,952 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 0.78 ( 46361 hom., cov: 32)
Exomes 𝑓: 0.79 ( 277591 hom. )
Consequence
TCP1
NM_030752.3 intron
NM_030752.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0570
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=-0.88).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.829 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TCP1 | NM_030752.3 | c.489-112G>T | intron_variant | ENST00000321394.12 | |||
TCP1 | NM_001008897.2 | c.24-112G>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TCP1 | ENST00000321394.12 | c.489-112G>T | intron_variant | 1 | NM_030752.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.778 AC: 118330AN: 152056Hom.: 46333 Cov.: 32
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GnomAD4 exome AF: 0.792 AC: 696204AN: 878588Hom.: 277591 Cov.: 11 AF XY: 0.795 AC XY: 364706AN XY: 458990
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GnomAD4 genome ? AF: 0.778 AC: 118410AN: 152176Hom.: 46361 Cov.: 32 AF XY: 0.781 AC XY: 58141AN XY: 74406
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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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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at