rs4962416

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_022802.3(CTBP2):​c.1679-4811A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.228 in 152,154 control chromosomes in the GnomAD database, including 4,414 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 0.23 ( 4414 hom., cov: 33)

Consequence

CTBP2
NM_022802.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.08
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 -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.01).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.303 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CTBP2NM_022802.3 linkuse as main transcriptc.1679-4811A>G intron_variant ENST00000309035.11

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CTBP2ENST00000309035.11 linkuse as main transcriptc.1679-4811A>G intron_variant 1 NM_022802.3 P56545-2

Frequencies

GnomAD3 genomes
AF:
0.228
AC:
34723
AN:
152038
Hom.:
4415
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.167
Gnomad AMI
AF:
0.364
Gnomad AMR
AF:
0.225
Gnomad ASJ
AF:
0.309
Gnomad EAS
AF:
0.00967
Gnomad SAS
AF:
0.317
Gnomad FIN
AF:
0.149
Gnomad MID
AF:
0.367
Gnomad NFE
AF:
0.282
Gnomad OTH
AF:
0.255
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.228
AC:
34731
AN:
152154
Hom.:
4414
Cov.:
33
AF XY:
0.223
AC XY:
16593
AN XY:
74388
show subpopulations
Gnomad4 AFR
AF:
0.167
Gnomad4 AMR
AF:
0.225
Gnomad4 ASJ
AF:
0.309
Gnomad4 EAS
AF:
0.00969
Gnomad4 SAS
AF:
0.316
Gnomad4 FIN
AF:
0.149
Gnomad4 NFE
AF:
0.282
Gnomad4 OTH
AF:
0.253
Alfa
AF:
0.275
Hom.:
11112
Bravo
AF:
0.229
Asia WGS
AF:
0.128
AC:
445
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
2.1
DANN
Benign
0.81

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: rs4962416; hg19: chr10-126696872; COSMIC: COSV58332887; COSMIC: COSV58332887; API