17-79795096-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_020649.3(CBX8):c.709G>A(p.Gly237Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000565 in 1,611,586 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_020649.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CBX8 | ENST00000269385.9 | c.709G>A | p.Gly237Arg | missense_variant | Exon 5 of 5 | 1 | NM_020649.3 | ENSP00000269385.4 | ||
CBX8 | ENST00000413392.5 | c.679G>A | p.Gly227Arg | missense_variant | Exon 5 of 5 | 3 | ENSP00000405058.1 | |||
CBX8 | ENST00000427800.2 | c.*108G>A | downstream_gene_variant | 2 | ENSP00000408753.2 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152190Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000245 AC: 6AN: 245372Hom.: 0 AF XY: 0.0000226 AC XY: 3AN XY: 132930
GnomAD4 exome AF: 0.0000582 AC: 85AN: 1459396Hom.: 0 Cov.: 35 AF XY: 0.0000524 AC XY: 38AN XY: 725712
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152190Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74360
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.709G>A (p.G237R) alteration is located in exon 5 (coding exon 5) of the CBX8 gene. This alteration results from a G to A substitution at nucleotide position 709, causing the glycine (G) at amino acid position 237 to be replaced by an arginine (R). 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