1-156310969-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PP3_ModerateBS2
The NM_005998.5(CCT3):c.1382G>A(p.Arg461His) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000316 in 1,613,904 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 (★).
Frequency
Consequence
NM_005998.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CCT3 | NM_005998.5 | c.1382G>A | p.Arg461His | missense_variant | Exon 12 of 14 | ENST00000295688.8 | NP_005989.3 | |
CCT3 | NM_001008800.3 | c.1268G>A | p.Arg423His | missense_variant | Exon 10 of 12 | NP_001008800.1 | ||
CCT3 | NR_036564.2 | n.1652G>A | non_coding_transcript_exon_variant | Exon 13 of 15 | ||||
CCT3 | NR_036565.2 | n.1603G>A | non_coding_transcript_exon_variant | Exon 13 of 15 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152152Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 251006Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135632
GnomAD4 exome AF: 0.0000315 AC: 46AN: 1461752Hom.: 0 Cov.: 33 AF XY: 0.0000330 AC XY: 24AN XY: 727172
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152152Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74320
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1382G>A (p.R461H) alteration is located in exon 12 (coding exon 12) of the CCT3 gene. This alteration results from a G to A substitution at nucleotide position 1382, causing the arginine (R) at amino acid position 461 to be replaced by a histidine (H). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at