rs4962424
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000337195.11(CTBP2):c.-101-2490A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.301 in 151,840 control chromosomes in the GnomAD database, including 7,021 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 0.30 ( 7021 hom., cov: 29)
Consequence
CTBP2
ENST00000337195.11 intron
ENST00000337195.11 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.644
Publications
5 publications found
Genes affected
CTBP2 (HGNC:2495): (C-terminal binding protein 2) This gene produces alternative transcripts encoding two distinct proteins. One protein is a transcriptional repressor, while the other isoform is a major component of specialized synapses known as synaptic ribbons. Both proteins contain a NAD+ binding domain similar to NAD+-dependent 2-hydroxyacid dehydrogenases. A portion of the 3' untranslated region was used to map this gene to chromosome 21q21.3; however, it was noted that similar loci elsewhere in the genome are likely. Blast analysis shows that this gene is present on chromosome 10. Several transcript variants encoding two different isoforms have been found for this gene. [provided by RefSeq, Feb 2014]
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ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.95).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.328 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CTBP2 | NM_001083914.3 | c.-101-2490A>T | intron_variant | Intron 2 of 10 | NP_001077383.1 | |||
CTBP2 | NM_001290214.3 | c.-101-2490A>T | intron_variant | Intron 2 of 10 | NP_001277143.1 | |||
CTBP2 | NM_001290215.3 | c.-101-2490A>T | intron_variant | Intron 2 of 10 | NP_001277144.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.301 AC: 45650AN: 151720Hom.: 7019 Cov.: 29 show subpopulations
GnomAD3 genomes
AF:
AC:
45650
AN:
151720
Hom.:
Cov.:
29
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.301 AC: 45684AN: 151840Hom.: 7021 Cov.: 29 AF XY: 0.300 AC XY: 22267AN XY: 74180 show subpopulations
GnomAD4 genome
AF:
AC:
45684
AN:
151840
Hom.:
Cov.:
29
AF XY:
AC XY:
22267
AN XY:
74180
show subpopulations
African (AFR)
AF:
AC:
10975
AN:
41386
American (AMR)
AF:
AC:
5120
AN:
15260
Ashkenazi Jewish (ASJ)
AF:
AC:
1155
AN:
3470
East Asian (EAS)
AF:
AC:
1699
AN:
5138
South Asian (SAS)
AF:
AC:
1167
AN:
4790
European-Finnish (FIN)
AF:
AC:
2814
AN:
10538
Middle Eastern (MID)
AF:
AC:
96
AN:
292
European-Non Finnish (NFE)
AF:
AC:
21653
AN:
67948
Other (OTH)
AF:
AC:
649
AN:
2106
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.523
Heterozygous variant carriers
0
1622
3243
4865
6486
8108
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
464
928
1392
1856
2320
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
904
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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