chr5-10981586-A-AACAC
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2
The NM_001332.4(CTNND2):c.3417+186_3417+187insGTGT variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0064 ( 8 hom., cov: 20)
Consequence
CTNND2
NM_001332.4 intron
NM_001332.4 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -1.53
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
?
Variant 5-10981586-A-AACAC is Benign according to our data. Variant chr5-10981586-A-AACAC is described in ClinVar as [Likely_benign]. Clinvar id is 1318181.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00637 (958/150460) while in subpopulation AFR AF= 0.0202 (832/41102). AF 95% confidence interval is 0.0191. There are 8 homozygotes in gnomad4. There are 463 alleles in male gnomad4 subpopulation. Median coverage is 20. This position pass quality control queck.
BS2
?
High AC in GnomAd at 961 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CTNND2 | NM_001332.4 | c.3417+186_3417+187insGTGT | intron_variant | ENST00000304623.13 | |||
LOC105374654 | XR_925791.3 | n.536-2579_536-2576dup | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CTNND2 | ENST00000304623.13 | c.3417+186_3417+187insGTGT | intron_variant | 1 | NM_001332.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00639 AC: 961AN: 150352Hom.: 8 Cov.: 20
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GnomAD4 genome ? AF: 0.00637 AC: 958AN: 150460Hom.: 8 Cov.: 20 AF XY: 0.00630 AC XY: 463AN XY: 73434
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 05, 2020 | - - |
Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at