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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.644

Publications

5 publications found
Variant links:
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]

Genome browser will be placed here

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
CTBP2NM_001083914.3 linkc.-101-2490A>T intron_variant Intron 2 of 10 NP_001077383.1 P56545-1
CTBP2NM_001290214.3 linkc.-101-2490A>T intron_variant Intron 2 of 10 NP_001277143.1 P56545-1
CTBP2NM_001290215.3 linkc.-101-2490A>T intron_variant Intron 2 of 10 NP_001277144.1 P56545-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CTBP2ENST00000337195.11 linkc.-101-2490A>T intron_variant Intron 2 of 10 1 ENSP00000338615.5 P56545-1

Frequencies

GnomAD3 genomes
AF:
0.301
AC:
45650
AN:
151720
Hom.:
7019
Cov.:
29
show subpopulations
Gnomad AFR
AF:
0.265
Gnomad AMI
AF:
0.390
Gnomad AMR
AF:
0.335
Gnomad ASJ
AF:
0.333
Gnomad EAS
AF:
0.330
Gnomad SAS
AF:
0.244
Gnomad FIN
AF:
0.267
Gnomad MID
AF:
0.309
Gnomad NFE
AF:
0.319
Gnomad OTH
AF:
0.311
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.301
AC:
45684
AN:
151840
Hom.:
7021
Cov.:
29
AF XY:
0.300
AC XY:
22267
AN XY:
74180
show subpopulations
African (AFR)
AF:
0.265
AC:
10975
AN:
41386
American (AMR)
AF:
0.336
AC:
5120
AN:
15260
Ashkenazi Jewish (ASJ)
AF:
0.333
AC:
1155
AN:
3470
East Asian (EAS)
AF:
0.331
AC:
1699
AN:
5138
South Asian (SAS)
AF:
0.244
AC:
1167
AN:
4790
European-Finnish (FIN)
AF:
0.267
AC:
2814
AN:
10538
Middle Eastern (MID)
AF:
0.329
AC:
96
AN:
292
European-Non Finnish (NFE)
AF:
0.319
AC:
21653
AN:
67948
Other (OTH)
AF:
0.308
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:
0.306
Hom.:
926
Bravo
AF:
0.308
Asia WGS
AF:
0.259
AC:
904
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.95
CADD
Benign
0.64
DANN
Benign
0.60
PhyloP100
-0.64
Mutation Taster
=100/0
polymorphism (auto)

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs4962424; hg19: chr10-126730214; API