chr7-56062691-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001762.4(CCT6A):āc.1459A>Gā(p.Met487Val) variant causes a missense change. The variant allele was found at a frequency of 0.0000434 in 1,613,864 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. M487T) has been classified as Uncertain significance.
Frequency
Consequence
NM_001762.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCT6A | NM_001762.4 | c.1459A>G | p.Met487Val | missense_variant | 13/14 | ENST00000275603.9 | |
CCT6A | NM_001009186.2 | c.1324A>G | p.Met442Val | missense_variant | 12/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCT6A | ENST00000275603.9 | c.1459A>G | p.Met487Val | missense_variant | 13/14 | 1 | NM_001762.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152230Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000438 AC: 11AN: 251420Hom.: 0 AF XY: 0.0000442 AC XY: 6AN XY: 135882
GnomAD4 exome AF: 0.0000424 AC: 62AN: 1461634Hom.: 0 Cov.: 30 AF XY: 0.0000371 AC XY: 27AN XY: 727144
GnomAD4 genome AF: 0.0000526 AC: 8AN: 152230Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74378
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 03, 2023 | The c.1459A>G (p.M487V) alteration is located in exon 13 (coding exon 13) of the CCT6A gene. This alteration results from a A to G substitution at nucleotide position 1459, causing the methionine (M) at amino acid position 487 to be replaced by a valine (V). 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