22-39134464-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_175709.5(CBX7):c.535G>T(p.Ala179Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,455,952 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 (★).
Frequency
Consequence
NM_175709.5 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CBX7 | NM_175709.5 | c.535G>T | p.Ala179Ser | missense_variant | Exon 5 of 6 | ENST00000216133.10 | NP_783640.1 | |
CBX7 | NM_001346743.2 | c.535G>T | p.Ala179Ser | missense_variant | Exon 5 of 6 | NP_001333672.1 | ||
CBX7 | NM_001346744.2 | c.256G>T | p.Ala86Ser | missense_variant | Exon 5 of 6 | NP_001333673.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1455952Hom.: 0 Cov.: 32 AF XY: 0.00000138 AC XY: 1AN XY: 724562
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.535G>T (p.A179S) alteration is located in exon 5 (coding exon 5) of the CBX7 gene. This alteration results from a G to T substitution at nucleotide position 535, causing the alanine (A) at amino acid position 179 to be replaced by a serine (S). 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