rs121908255
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 3P and 1B. PM2PP5BP4
The ENST00000310942.9(CBX2):c.293C>T(p.Pro98Leu) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P98A) has been classified as Uncertain significance.
Frequency
Consequence
ENST00000310942.9 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CBX2 | NM_005189.3 | c.293C>T | p.Pro98Leu | missense_variant | 5/5 | ENST00000310942.9 | NP_005180.1 | |
CBX2 | XM_011525382.2 | c.293C>T | p.Pro98Leu | missense_variant | 5/6 | XP_011523684.1 | ||
CBX2 | XM_011525383.3 | c.38C>T | p.Pro13Leu | missense_variant | 5/6 | XP_011523685.1 | ||
CBX2 | XM_047436946.1 | c.38C>T | p.Pro13Leu | missense_variant | 4/5 | XP_047292902.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CBX2 | ENST00000310942.9 | c.293C>T | p.Pro98Leu | missense_variant | 5/5 | 1 | NM_005189.3 | ENSP00000308750 | P1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Cov.: 30
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
46,XY sex reversal 5 Pathogenic:1Other:1
not provided, no classification provided | literature only | UniProtKB/Swiss-Prot | - | - - |
Pathogenic, no assertion criteria provided | literature only | OMIM | May 01, 2009 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at