chr11-125957023-A-G
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_001378964.1(CDON):c.*3919T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00354 in 238,100 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0038 ( 3 hom., cov: 33)
Exomes 𝑓: 0.0031 ( 3 hom. )
Consequence
CDON
NM_001378964.1 3_prime_UTR
NM_001378964.1 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0110
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=-0.85).
BP6
Variant 11-125957023-A-G is Benign according to our data. Variant chr11-125957023-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 303376.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.00377 (574/152326) while in subpopulation NFE AF= 0.00422 (287/68028). AF 95% confidence interval is 0.00382. There are 3 homozygotes in gnomad4. There are 271 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
High AC in GnomAd4 at 574 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CDON | NM_001378964.1 | c.*3919T>C | 3_prime_UTR_variant | 20/20 | ENST00000531738.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CDON | ENST00000531738.6 | c.*3919T>C | 3_prime_UTR_variant | 20/20 | 1 | NM_001378964.1 | P1 | ||
CDON | ENST00000392693.7 | c.*3919T>C | 3_prime_UTR_variant | 20/20 | 1 | ||||
VSIG10L2 | ENST00000638636.2 | c.*1109A>G | 3_prime_UTR_variant | 10/10 | 5 | A2 | |||
CDON | ENST00000684078.1 | c.*3919T>C | 3_prime_UTR_variant | 20/20 |
Frequencies
GnomAD3 genomes AF: 0.00378 AC: 575AN: 152208Hom.: 3 Cov.: 33
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GnomAD4 exome AF: 0.00315 AC: 270AN: 85774Hom.: 3 Cov.: 5 AF XY: 0.00324 AC XY: 134AN XY: 41338
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GnomAD4 genome AF: 0.00377 AC: 574AN: 152326Hom.: 3 Cov.: 33 AF XY: 0.00364 AC XY: 271AN XY: 74486
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Holoprosencephaly 11 Benign:1
Likely 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 likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease. - |
Computational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at