17-79779686-A-G
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_005189.3(CBX2):c.182+259A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.109 in 531,454 control chromosomes in the GnomAD database, including 3,687 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.10 ( 994 hom., cov: 34)
Exomes 𝑓: 0.11 ( 2693 hom. )
Consequence
CBX2
NM_005189.3 intron
NM_005189.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.198
Genes affected
CBX2 (HGNC:1552): (chromobox 2) This gene encodes a component of the polycomb multiprotein complex, which is required to maintain the transcriptionally repressive state of many genes throughout development via chromatin remodeling and modification of histones. Disruption of this gene in mice results in male-to-female gonadal sex reversal. Mutations in this gene are also associated with gonadal dysgenesis in humans. Alternatively spliced transcript variants encoding different isoforms have been noted for this gene.[provided by RefSeq, Mar 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.81).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.177 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CBX2 | NM_005189.3 | c.182+259A>G | intron_variant | ENST00000310942.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CBX2 | ENST00000310942.9 | c.182+259A>G | intron_variant | 1 | NM_005189.3 | P1 | |||
CBX2 | ENST00000269399.5 | c.182+259A>G | intron_variant | 1 | |||||
CBX2 | ENST00000571484.1 | n.514A>G | non_coding_transcript_exon_variant | 3/3 | 1 |
Frequencies
GnomAD3 genomes AF: 0.101 AC: 15354AN: 152180Hom.: 987 Cov.: 34
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GnomAD4 exome AF: 0.112 AC: 42554AN: 379156Hom.: 2693 Cov.: 0 AF XY: 0.111 AC XY: 22024AN XY: 198336
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GnomAD4 genome AF: 0.101 AC: 15377AN: 152298Hom.: 994 Cov.: 34 AF XY: 0.104 AC XY: 7723AN XY: 74476
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at