22-39134490-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_175709.5(CBX7):c.509G>A(p.Arg170Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000186 in 1,611,000 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_175709.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CBX7 | NM_175709.5 | c.509G>A | p.Arg170Gln | missense_variant | Exon 5 of 6 | ENST00000216133.10 | NP_783640.1 | |
CBX7 | NM_001346743.2 | c.509G>A | p.Arg170Gln | missense_variant | Exon 5 of 6 | NP_001333672.1 | ||
CBX7 | NM_001346744.2 | c.247-17G>A | intron_variant | Intron 4 of 5 | NP_001333673.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152220Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000411 AC: 1AN: 243032Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 132734
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1458780Hom.: 0 Cov.: 32 AF XY: 0.00000138 AC XY: 1AN XY: 725842
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152220Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74368
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.509G>A (p.R170Q) alteration is located in exon 5 (coding exon 5) of the CBX7 gene. This alteration results from a G to A substitution at nucleotide position 509, causing the arginine (R) at amino acid position 170 to be replaced by a glutamine (Q). 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