rs4962416
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_022802(CTBP2):c.1679-4811A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.228 in 152038 control chromosomes in the gnomAD Genomes database, including 4415 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 0.23 ( 4415 hom., cov: 33)
Consequence
CTBP2
NM_022802 intron
NM_022802 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.08
Links
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-1.01).
BA1
?
GnomAd highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.304 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CTBP2 | NM_022802.3 | c.1679-4811A>G | intron_variant | ENST00000309035.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CTBP2 | ENST00000309035.11 | c.1679-4811A>G | intron_variant | 1 | NM_022802.3 |
Frequencies
GnomAD3 genomes AF: 0.228 AC: 34723AN: 152038Hom.: 4415 Cov.: 33
GnomAD3 genomes
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34723
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152038
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Cov.:
33
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Asia WGS
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445
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Find out SpliceAI and Pangolin per-transcript scores at