chr11-125957112-C-T
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001378964.1(CDON):c.*3830G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0228 in 153,066 control chromosomes in the GnomAD database, including 150 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.023 ( 150 hom., cov: 32)
Exomes 𝑓: 0.0035 ( 0 hom. )
Consequence
CDON
NM_001378964.1 3_prime_UTR
NM_001378964.1 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.628
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]
VSIG10L2 (HGNC:27879): (V-set and immunoglobulin domain containing 10 like 2) Predicted to enable cell adhesion molecule binding activity. Predicted to be involved in cell-cell adhesion. Predicted to be active in cell-cell junction. Predicted to be integral component of plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BP6
Variant 11-125957112-C-T is Benign according to our data. Variant chr11-125957112-C-T is described in ClinVar as [Benign]. Clinvar id is 303380.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0771 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CDON | NM_001378964.1 | c.*3830G>A | 3_prime_UTR_variant | 20/20 | ENST00000531738.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CDON | ENST00000531738.6 | c.*3830G>A | 3_prime_UTR_variant | 20/20 | 1 | NM_001378964.1 | P1 | ||
CDON | ENST00000392693.7 | c.*3830G>A | 3_prime_UTR_variant | 20/20 | 1 | ||||
VSIG10L2 | ENST00000638636.2 | c.*1198C>T | 3_prime_UTR_variant | 10/10 | 5 | A2 | |||
CDON | ENST00000684078.1 | c.*3830G>A | 3_prime_UTR_variant | 20/20 |
Frequencies
GnomAD3 genomes AF: 0.0228 AC: 3475AN: 152082Hom.: 149 Cov.: 32
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GnomAD4 exome AF: 0.00346 AC: 3AN: 866Hom.: 0 Cov.: 3 AF XY: 0.00446 AC XY: 2AN XY: 448
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GnomAD4 genome AF: 0.0229 AC: 3486AN: 152200Hom.: 150 Cov.: 32 AF XY: 0.0219 AC XY: 1629AN XY: 74436
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Holoprosencephaly 11 Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 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
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at