rs3737336
Positions:
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1
The NM_001378964.1(CDON):c.*140A>G variant causes a 3 prime UTR change. The variant allele was found at a frequency of 0.293 in 790,096 control chromosomes in the GnomAD database, including 35,027 homozygotes. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.25 ( 5477 hom., cov: 32)
Exomes 𝑓: 0.30 ( 29550 hom. )
Consequence
CDON
NM_001378964.1 3_prime_UTR
NM_001378964.1 3_prime_UTR
Scores
1
1
Clinical Significance
Conservation
PhyloP100: 4.78
Genes affected
CDON (HGNC:17104): (cell adhesion associated, oncogene regulated) This gene encodes a cell surface receptor that is a member of the immunoglobulin superfamily. The encoded protein contains three fibronectin type III domains and five immunoglobulin-like C2-type domains. This protein is a member of a cell-surface receptor complex that mediates cell-cell interactions between muscle precursor cells and positively regulates myogenesis. [provided by RefSeq, Aug 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -16 ACMG points.
BP6
?
Variant 11-125960802-T-C is Benign according to our data. Variant chr11-125960802-T-C is described in ClinVar as [Benign]. Clinvar id is 303488.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.309 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CDON | NM_001378964.1 | c.*140A>G | 3_prime_UTR_variant | 20/20 | ENST00000531738.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CDON | ENST00000531738.6 | c.*140A>G | 3_prime_UTR_variant | 20/20 | 1 | NM_001378964.1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.255 AC: 38761AN: 152022Hom.: 5475 Cov.: 32
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GnomAD4 exome AF: 0.302 AC: 192349AN: 637956Hom.: 29550 Cov.: 8 AF XY: 0.304 AC XY: 103436AN XY: 340620
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GnomAD4 genome ? AF: 0.255 AC: 38780AN: 152140Hom.: 5477 Cov.: 32 AF XY: 0.257 AC XY: 19095AN XY: 74356
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Apr 12, 2019 | - - |
Holoprosencephaly 11 Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 12, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
Computational scores
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Name
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BayesDel_noAF
Uncertain
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at