chr10-125050460-A-G

Variant names:

• chr10-125050460-A-G
• rs718949
• NM_001329.4:c.-101-11305T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001329.4(CTBP2):​c.-101-11305T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.295 in 152,214 control chromosomes in the GnomAD database, including 7,724 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 (7724 hom., cov: 33)
• Consequence: CTBP2 NM_001329.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.668
• Publications: 10 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.476 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001329.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CTBP2	NM_001329.4	MANE Select	c.-101-11305T>C		intron	N/A	NP_001320.1
	CTBP2	NM_001083914.3		c.-101-11305T>C		intron	N/A	NP_001077383.1
	CTBP2	NM_001290214.3		c.-101-11305T>C		intron	N/A	NP_001277143.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CTBP2	ENST00000337195.11	TSL:1 MANE Select	c.-101-11305T>C		intron	N/A	ENSP00000338615.5
	CTBP2	ENST00000411419.7	TSL:1	c.-101-11305T>C		intron	N/A	ENSP00000410474.2
	CTBP2	ENST00000494626.6	TSL:1	c.-101-11305T>C		intron	N/A	ENSP00000436285.1

Frequencies

GnomAD3 genomes AF: 0.295 AC: 44871 AN: 152096 Hom.: 7703 Cov.: 33

Gnomad AFR AF: 0.482

Gnomad AMI AF: 0.160

Gnomad AMR AF: 0.261

Gnomad ASJ AF: 0.231

Gnomad EAS AF: 0.0437

Gnomad SAS AF: 0.280

Gnomad FIN AF: 0.208

Gnomad MID AF: 0.287

Gnomad NFE AF: 0.229

Gnomad OTH AF: 0.282

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

GnomAD4 genome AF: 0.295 AC: 44929 AN: 152214 Hom.: 7724 Cov.: 33 AF XY: 0.292 AC XY: 21748 AN XY: 74416

African (AFR) AF: 0.482 AC: 19996 AN: 41508

American (AMR) AF: 0.261 AC: 3988 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.231 AC: 800 AN: 3466

East Asian (EAS) AF: 0.0438 AC: 227 AN: 5178

South Asian (SAS) AF: 0.279 AC: 1346 AN: 4826

European-Finnish (FIN) AF: 0.208 AC: 2204 AN: 10612

Middle Eastern (MID) AF: 0.295 AC: 86 AN: 292

European-Non Finnish (NFE) AF: 0.229 AC: 15548 AN: 68004

Other (OTH) AF: 0.278 AC: 588 AN: 2116

Alfa AF: 0.244 Hom.: 10352

Bravo AF: 0.304

Asia WGS AF: 0.166 AC: 581 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.032
DANN	Benign	0.26
PhyloP100		-0.67
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.2
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs718949; hg19: chr10-126739029;