chr5-10981767-C-CTTTA
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2
The NM_001332.4(CTNND2):c.3417+5_3417+6insTAAA variant causes a splice donor region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0198 in 1,609,804 control chromosomes in the GnomAD database, including 438 homozygotes. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.017 ( 42 hom., cov: 33)
Exomes 𝑓: 0.020 ( 396 hom. )
Consequence
CTNND2
NM_001332.4 splice_donor_region, intron
NM_001332.4 splice_donor_region, intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -0.479
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 5-10981767-C-CTTTA is Benign according to our data. Variant chr5-10981767-C-CTTTA is described in ClinVar as [Benign]. Clinvar id is 1292997.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0166 (2526/152256) while in subpopulation NFE AF= 0.0197 (1340/68022). AF 95% confidence interval is 0.0188. There are 42 homozygotes in gnomad4. There are 1367 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High AC in GnomAd at 2519 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CTNND2 | NM_001332.4 | c.3417+5_3417+6insTAAA | splice_donor_region_variant, intron_variant | ENST00000304623.13 | |||
LOC105374654 | XR_925791.3 | n.536-2415_536-2412dup | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CTNND2 | ENST00000304623.13 | c.3417+5_3417+6insTAAA | splice_donor_region_variant, intron_variant | 1 | NM_001332.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0166 AC: 2519AN: 152138Hom.: 41 Cov.: 33
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GnomAD3 exomes AF: 0.0179 AC: 4475AN: 250228Hom.: 81 AF XY: 0.0173 AC XY: 2344AN XY: 135174
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GnomAD4 exome AF: 0.0201 AC: 29299AN: 1457548Hom.: 396 Cov.: 29 AF XY: 0.0196 AC XY: 14190AN XY: 725198
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GnomAD4 genome ? AF: 0.0166 AC: 2526AN: 152256Hom.: 42 Cov.: 33 AF XY: 0.0184 AC XY: 1367AN XY: 74432
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Aug 28, 2018 | - - |
Computational scores
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Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at