Genetic Variant CTBP2:c.1678+10C>G (chr10-125026072-G-C) – ACMG Classification: Benign (-13 pts)

Variant summary

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

The NM_022802.3(CTBP2):c.1678+10C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0318 in 1,548,982 control chromosomes in the GnomAD database, including 987 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.025 ( 67 hom., cov: 33)

Exomes 𝑓: 0.033 ( 920 hom. )

Consequence

CTBP2
NM_022802.3 intron

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: 1.61

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]

CTBP2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.76).

BP6

Variant 10-125026072-G-C is Benign according to our data. Variant chr10-125026072-G-C is described in ClinVar as [Benign]. Clinvar id is 3060493.Status of the report is no_assertion_criteria_provided, 0 stars.

BA1

GnomAdExome4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0563 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CTBP2	NM_022802.3 link	c.1678+10C>G		intron_variant	Intron 1 of 8	ENST00000309035.11	NP_073713.2	P56545-2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CTBP2	ENST00000309035.11 link	c.1678+10C>G		intron_variant	Intron 1 of 8	1	NM_022802.3	ENSP00000311825.6		P56545-2
CTBP2	ENST00000337195.10 link	c.58+12925C>G		intron_variant	Intron 3 of 10	1		ENSP00000338615.5		P56545-1

Frequencies

GnomAD3 genomes

AF:

0.0248

AC:

3780

AN:

152188

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00572

Gnomad AMI

AF:

0.00110

Gnomad AMR

AF:

0.0374

Gnomad ASJ

AF:

0.0452

Gnomad EAS

AF:

0.0392

Gnomad SAS

AF:

0.0549

Gnomad FIN

AF:

0.0166

Gnomad MID

AF:

0.0380

Gnomad NFE

AF:

0.0307

Gnomad OTH

AF:

0.0344

GnomAD3 exomes

AF:

0.0331

AC:

6811

AN:

205470

Hom.:

159

AF XY:

0.0341

AC XY:

3700

AN XY:

108620

show subpopulations

Gnomad AFR exome

AF:

0.00568

Gnomad AMR exome

AF:

0.0423

Gnomad ASJ exome

AF:

0.0360

Gnomad EAS exome

AF:

0.0294

Gnomad SAS exome

AF:

0.0543

Gnomad FIN exome

AF:

0.0200

Gnomad NFE exome

AF:

0.0331

Gnomad OTH exome

AF:

0.0374

GnomAD4 exome

AF:

0.0325

AC:

45441

AN:

1396676

Hom.:

920

Cov.:

AF XY:

0.0333

AC XY:

22802

AN XY:

685010

show subpopulations

Gnomad4 AFR exome

AF:

0.00485

Gnomad4 AMR exome

AF:

0.0435

Gnomad4 ASJ exome

AF:

0.0364

Gnomad4 EAS exome

AF:

0.0583

Gnomad4 SAS exome

AF:

0.0543

Gnomad4 FIN exome

AF:

0.0226

Gnomad4 NFE exome

AF:

0.0306

Gnomad4 OTH exome

AF:

0.0359

GnomAD4 genome

AF:

0.0249

AC:

3794

AN:

152306

Hom.:

Cov.:

AF XY:

0.0255

AC XY:

1900

AN XY:

74478

show subpopulations

Gnomad4 AFR

AF:

0.00573

Gnomad4 AMR

AF:

0.0372

Gnomad4 ASJ

AF:

0.0452

Gnomad4 EAS

AF:

0.0393

Gnomad4 SAS

AF:

0.0550

Gnomad4 FIN

AF:

0.0166

Gnomad4 NFE

AF:

0.0307

Gnomad4 OTH

AF:

0.0406

Alfa

AF:

0.0181

Hom.:

Bravo

AF:

0.0237

Asia WGS

AF:

0.0810

AC:

283

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

CTBP2-related disorder

Benign:1

Jul 11, 2019

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

This 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_noAF

Benign

-0.76

CADD

Benign

DANN

Benign

0.71

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over