rs3781409

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1

The ENST00000309035.11(CTBP2):​c.700G>A​(p.Val234Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.255 in 1,613,106 control chromosomes in the GnomAD database, including 53,878 homozygotes. In-silico tool predicts a benign outcome for this variant. 11/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.22 ( 3951 hom., cov: 33)
Exomes 𝑓: 0.26 ( 49927 hom. )

Consequence

CTBP2
ENST00000309035.11 missense

Scores

1
4
10

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: 3.06
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 made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.001383245).
BP6
Variant 10-125027060-C-T is Benign according to our data. Variant chr10-125027060-C-T is described in ClinVar as [Benign]. Clinvar id is 3059060.Status of the report is no_assertion_criteria_provided, 0 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.265 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
CTBP2NM_022802.3 linkuse as main transcriptc.700G>A p.Val234Met missense_variant 1/9 ENST00000309035.11 NP_073713.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
CTBP2ENST00000309035.11 linkuse as main transcriptc.700G>A p.Val234Met missense_variant 1/91 NM_022802.3 ENSP00000311825 P56545-2

Frequencies

GnomAD3 genomes
AF:
0.216
AC:
32917
AN:
152114
Hom.:
3951
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.121
Gnomad AMI
AF:
0.389
Gnomad AMR
AF:
0.248
Gnomad ASJ
AF:
0.246
Gnomad EAS
AF:
0.277
Gnomad SAS
AF:
0.183
Gnomad FIN
AF:
0.193
Gnomad MID
AF:
0.256
Gnomad NFE
AF:
0.264
Gnomad OTH
AF:
0.229
GnomAD3 exomes
AF:
0.240
AC:
59750
AN:
249338
Hom.:
7478
AF XY:
0.238
AC XY:
32126
AN XY:
135242
show subpopulations
Gnomad AFR exome
AF:
0.120
Gnomad AMR exome
AF:
0.266
Gnomad ASJ exome
AF:
0.243
Gnomad EAS exome
AF:
0.266
Gnomad SAS exome
AF:
0.180
Gnomad FIN exome
AF:
0.201
Gnomad NFE exome
AF:
0.267
Gnomad OTH exome
AF:
0.255
GnomAD4 exome
AF:
0.259
AC:
378277
AN:
1460874
Hom.:
49927
Cov.:
94
AF XY:
0.257
AC XY:
186631
AN XY:
726638
show subpopulations
Gnomad4 AFR exome
AF:
0.114
Gnomad4 AMR exome
AF:
0.264
Gnomad4 ASJ exome
AF:
0.246
Gnomad4 EAS exome
AF:
0.297
Gnomad4 SAS exome
AF:
0.183
Gnomad4 FIN exome
AF:
0.204
Gnomad4 NFE exome
AF:
0.271
Gnomad4 OTH exome
AF:
0.247
GnomAD4 genome
AF:
0.216
AC:
32924
AN:
152232
Hom.:
3951
Cov.:
33
AF XY:
0.214
AC XY:
15917
AN XY:
74446
show subpopulations
Gnomad4 AFR
AF:
0.121
Gnomad4 AMR
AF:
0.248
Gnomad4 ASJ
AF:
0.246
Gnomad4 EAS
AF:
0.277
Gnomad4 SAS
AF:
0.183
Gnomad4 FIN
AF:
0.193
Gnomad4 NFE
AF:
0.264
Gnomad4 OTH
AF:
0.226
Alfa
AF:
0.260
Hom.:
8072
Bravo
AF:
0.220
TwinsUK
AF:
0.279
AC:
1034
ALSPAC
AF:
0.285
AC:
1099
ESP6500AA
AF:
0.123
AC:
541
ESP6500EA
AF:
0.265
AC:
2280
ExAC
AF:
0.237
AC:
28836
Asia WGS
AF:
0.184
AC:
639
AN:
3478
EpiCase
AF:
0.267
EpiControl
AF:
0.272

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: no assertion criteria provided
LINK: link

Submissions by phenotype

CTBP2-related disorder Benign:1
Benign, no assertion criteria providedclinical testingPreventionGenetics, part of Exact SciencesOct 28, 2019This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
-0.46
T
BayesDel_noAF
Benign
-0.29
CADD
Benign
21
DANN
Pathogenic
1.0
Eigen
Benign
-0.014
Eigen_PC
Benign
0.081
FATHMM_MKL
Uncertain
0.82
D
LIST_S2
Benign
0.74
T
MetaRNN
Benign
0.0014
T
MetaSVM
Benign
-1.1
T
MutationTaster
Benign
0.025
P;P;P;P;P
PrimateAI
Uncertain
0.68
T
PROVEAN
Benign
-0.80
N
REVEL
Benign
0.21
Sift
Uncertain
0.0010
D
Sift4G
Uncertain
0.0080
D
Polyphen
0.21
B
Vest4
0.10
MPC
0.52
ClinPred
0.030
T
GERP RS
3.6
gMVP
0.22

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs3781409; hg19: chr10-126715629; COSMIC: COSV58339247; API