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

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.08

Links

CTBP2 (HGNC:2495):

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
CTBP2	NM_022802.3 linkuse as main transcript	c.1679-4811A>G		intron_variant		ENST00000309035.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CTBP2	ENST00000309035.11 linkuse as main transcript	c.1679-4811A>G		intron_variant		1	NM_022802.3		P56545-2

Frequencies

GnomAD3 genomes

AF:

0.228

AC:

34723

AN:

152038

Hom.:

4415

Cov.:

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Links

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over