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10-124993314-C-T

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1

The NM_022802.3(CTBP2):c.2547G>A(p.Pro849=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00326 in 1,608,626 control chromosomes in the GnomAD database, including 122 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.017 ( 68 hom., cov: 33)
Exomes 𝑓: 0.0018 ( 54 hom. )

Consequence

CTBP2
NM_022802.3 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -6.20
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.68).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 10-124993314-C-T is Benign according to our data. Variant chr10-124993314-C-T is described in ClinVar as [Benign]. Clinvar id is 779348.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=-6.2 with no splicing effect.
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0569 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CTBP2NM_022802.3 linkuse as main transcriptc.2547G>A p.Pro849= synonymous_variant 7/9 ENST00000309035.11

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CTBP2ENST00000309035.11 linkuse as main transcriptc.2547G>A p.Pro849= synonymous_variant 7/91 NM_022802.3 P56545-2

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0171
AC:
2601
AN:
152114
Hom.:
67
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0587
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00759
Gnomad ASJ
AF:
0.000289
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000207
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00316
Gnomad NFE
AF:
0.000323
Gnomad OTH
AF:
0.0139
GnomAD3 exomes
AF:
0.00456
AC:
1145
AN:
250838
Hom.:
26
AF XY:
0.00352
AC XY:
477
AN XY:
135616
show subpopulations
Gnomad AFR exome
AF:
0.0602
Gnomad AMR exome
AF:
0.00362
Gnomad ASJ exome
AF:
0.000199
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.000262
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000203
Gnomad OTH exome
AF:
0.00180
GnomAD4 exome
AF:
0.00181
AC:
2633
AN:
1456394
Hom.:
54
Cov.:
32
AF XY:
0.00163
AC XY:
1181
AN XY:
723530
show subpopulations
Gnomad4 AFR exome
AF:
0.0565
Gnomad4 AMR exome
AF:
0.00464
Gnomad4 ASJ exome
AF:
0.000115
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000151
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.000245
Gnomad4 OTH exome
AF:
0.00399
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0172
AC:
2614
AN:
152232
Hom.:
68
Cov.:
33
AF XY:
0.0163
AC XY:
1216
AN XY:
74416
show subpopulations
Gnomad4 AFR
AF:
0.0589
Gnomad4 AMR
AF:
0.00758
Gnomad4 ASJ
AF:
0.000289
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000207
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000323
Gnomad4 OTH
AF:
0.0137
Alfa
AF:
0.00784
Hom.:
14
Bravo
AF:
0.0200
Asia WGS
AF:
0.00520
AC:
18
AN:
3478
EpiCase
AF:
0.000383
EpiControl
AF:
0.000178

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeDec 26, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.68
Cadd
Benign
3.7
Dann
Benign
0.92

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: rs76804352; hg19: chr10-126681883; API