rs10794197

Positions:

• chr10-125086667-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001329.4(CTBP2):​c.-102+24323C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.209 in 149,230 control chromosomes in the GnomAD database, including 3,453 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 0.21 (3453 hom., cov: 29)
• Consequence: CTBP2 NM_001329.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.453

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.29 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CTBP2	NM_001083914.3	c.-102+24323C>T		intron_variant			NP_001077383.1
CTBP2	NM_001290214.3	c.-102+46845C>T		intron_variant			NP_001277143.1
CTBP2	NM_001290215.3	c.-102+24323C>T		intron_variant			NP_001277144.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CTBP2	ENST00000337195.10	c.-102+24323C>T		intron_variant		1		ENSP00000338615.5

Frequencies

GnomAD3 genomes AF: 0.209 AC: 31124 AN: 149150 Hom.: 3452 Cov.: 29

Gnomad AFR AF: 0.149

Gnomad AMI AF: 0.181

Gnomad AMR AF: 0.178

Gnomad ASJ AF: 0.316

Gnomad EAS AF: 0.0936

Gnomad SAS AF: 0.303

Gnomad FIN AF: 0.205

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.248

Gnomad OTH AF: 0.238

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.209 AC: 31133 AN: 149230 Hom.: 3453 Cov.: 29 AF XY: 0.208 AC XY: 15115 AN XY: 72620

Gnomad4 AFR AF: 0.149

Gnomad4 AMR AF: 0.178

Gnomad4 ASJ AF: 0.316

Gnomad4 EAS AF: 0.0935

Gnomad4 SAS AF: 0.303

Gnomad4 FIN AF: 0.205

Gnomad4 NFE AF: 0.248

Gnomad4 OTH AF: 0.238

Alfa AF: 0.245 Hom.: 6528

Bravo AF: 0.200

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.7
DANN	Benign	0.60

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

Other links and lift over

dbSNP: rs10794197; hg19: chr10-126775236;