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GeneBe

rs4962416

Variant summary

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

The NM_022802(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 152038 control chromosomes in the gnomAD Genomes database, including 4415 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 ( 4415 hom., cov: 33)

Consequence

CTBP2
NM_022802 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.08

Links

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
?
GnomAd highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.304 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
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

Find out SpliceAI 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;