chr5-11489403-T-C
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001332.4(CTNND2):c.287+75541A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.273 in 152,080 control chromosomes in the GnomAD database, including 5,980 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 0.27 ( 5980 hom., cov: 33)
Consequence
CTNND2
NM_001332.4 intron
NM_001332.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.447
Publications
1 publications found
Genes affected
CTNND2 (HGNC:2516): (catenin delta 2) This gene encodes an adhesive junction associated protein of the armadillo/beta-catenin superfamily and is implicated in brain and eye development and cancer formation. The protein encoded by this gene promotes the disruption of E-cadherin based adherens junction to favor cell spreading upon stimulation by hepatocyte growth factor. This gene is overexpressed in prostate adenocarcinomas and is associated with decreased expression of tumor suppressor E-cadherin in this tissue. This gene resides in a region of the short arm of chromosome 5 that is deleted in Cri du Chat syndrome. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Dec 2013]
CTNND2 Gene-Disease associations (from GenCC):
- complex neurodevelopmental disorderInheritance: AD Classification: STRONG Submitted by: Illumina
- neurodevelopmental disorderInheritance: AD Classification: STRONG Submitted by: G2P
- benign adult familial myoclonic epilepsyInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
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ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.384 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.273 AC: 41497AN: 151964Hom.: 5975 Cov.: 33 show subpopulations
GnomAD3 genomes
AF:
AC:
41497
AN:
151964
Hom.:
Cov.:
33
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.273 AC: 41525AN: 152080Hom.: 5980 Cov.: 33 AF XY: 0.282 AC XY: 20997AN XY: 74344 show subpopulations
GnomAD4 genome
AF:
AC:
41525
AN:
152080
Hom.:
Cov.:
33
AF XY:
AC XY:
20997
AN XY:
74344
show subpopulations
African (AFR)
AF:
AC:
8271
AN:
41492
American (AMR)
AF:
AC:
4683
AN:
15274
Ashkenazi Jewish (ASJ)
AF:
AC:
979
AN:
3470
East Asian (EAS)
AF:
AC:
938
AN:
5174
South Asian (SAS)
AF:
AC:
1920
AN:
4814
European-Finnish (FIN)
AF:
AC:
4493
AN:
10562
Middle Eastern (MID)
AF:
AC:
88
AN:
294
European-Non Finnish (NFE)
AF:
AC:
19462
AN:
67974
Other (OTH)
AF:
AC:
537
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
1528
3056
4585
6113
7641
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
928
AN:
3476
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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