rs149067488
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_012073.5(CCT5):c.1310C>T(p.Ala437Val) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000397 in 1,614,020 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 (★). Synonymous variant affecting the same amino acid position (i.e. A437A) has been classified as Likely benign.
Frequency
Consequence
NM_012073.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCT5 | NM_012073.5 | c.1310C>T | p.Ala437Val | missense_variant | 9/11 | ENST00000280326.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCT5 | ENST00000280326.9 | c.1310C>T | p.Ala437Val | missense_variant | 9/11 | 1 | NM_012073.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152184Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000477 AC: 12AN: 251406Hom.: 0 AF XY: 0.0000515 AC XY: 7AN XY: 135888
GnomAD4 exome AF: 0.0000404 AC: 59AN: 1461836Hom.: 0 Cov.: 31 AF XY: 0.0000413 AC XY: 30AN XY: 727226
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152184Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74338
ClinVar
Submissions by phenotype
Hereditary sensory and autonomic neuropathy with spastic paraplegia Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Apr 08, 2023 | ClinVar contains an entry for this variant (Variation ID: 575826). This variant has not been reported in the literature in individuals affected with CCT5-related conditions. This variant is present in population databases (rs149067488, gnomAD 0.007%). This sequence change replaces alanine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 437 of the CCT5 protein (p.Ala437Val). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at