rs11557649
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_012073.5(CCT5):c.738G>A(p.Ala246=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0324 in 1,614,096 control chromosomes in the GnomAD database, including 1,000 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Synonymous variant affecting the same amino acid position (i.e. A246A) has been classified as Likely benign.
Frequency
Consequence
NM_012073.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCT5 | NM_012073.5 | c.738G>A | p.Ala246= | synonymous_variant | 6/11 | ENST00000280326.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCT5 | ENST00000280326.9 | c.738G>A | p.Ala246= | synonymous_variant | 6/11 | 1 | NM_012073.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0275 AC: 4186AN: 152158Hom.: 73 Cov.: 33
GnomAD3 exomes AF: 0.0273 AC: 6866AN: 251472Hom.: 136 AF XY: 0.0276 AC XY: 3755AN XY: 135916
GnomAD4 exome AF: 0.0329 AC: 48047AN: 1461820Hom.: 927 Cov.: 33 AF XY: 0.0325 AC XY: 23660AN XY: 727228
GnomAD4 genome ? AF: 0.0275 AC: 4187AN: 152276Hom.: 73 Cov.: 33 AF XY: 0.0279 AC XY: 2080AN XY: 74448
ClinVar
Submissions by phenotype
Hereditary sensory and autonomic neuropathy with spastic paraplegia Benign:2
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 03, 2015 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at