chr11-125957058-A-C
Position:
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001378964.1(CDON):c.*3884T>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.292 in 164,026 control chromosomes in the GnomAD database, including 7,494 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.29 ( 7034 hom., cov: 32)
Exomes 𝑓: 0.27 ( 460 hom. )
Consequence
CDON
NM_001378964.1 3_prime_UTR
NM_001378964.1 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.519
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BP6
Variant 11-125957058-A-C is Benign according to our data. Variant chr11-125957058-A-C is described in ClinVar as [Benign]. Clinvar id is 303378.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.337 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CDON | NM_001378964.1 | c.*3884T>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.*3884T>G | 3_prime_UTR_variant | 20/20 | 1 | NM_001378964.1 | P1 | ||
CDON | ENST00000392693.7 | c.*3884T>G | 3_prime_UTR_variant | 20/20 | 1 | ||||
VSIG10L2 | ENST00000638636.2 | c.*1144A>C | 3_prime_UTR_variant | 10/10 | 5 | A2 | |||
CDON | ENST00000684078.1 | c.*3884T>G | 3_prime_UTR_variant | 20/20 |
Frequencies
GnomAD3 genomes AF: 0.294 AC: 44685AN: 151954Hom.: 7023 Cov.: 32
GnomAD3 genomes
AF:
AC:
44685
AN:
151954
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.270 AC: 3233AN: 11954Hom.: 460 Cov.: 4 AF XY: 0.274 AC XY: 1606AN XY: 5860
GnomAD4 exome
AF:
AC:
3233
AN:
11954
Hom.:
Cov.:
4
AF XY:
AC XY:
1606
AN XY:
5860
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome AF: 0.294 AC: 44727AN: 152072Hom.: 7034 Cov.: 32 AF XY: 0.297 AC XY: 22043AN XY: 74314
GnomAD4 genome
AF:
AC:
44727
AN:
152072
Hom.:
Cov.:
32
AF XY:
AC XY:
22043
AN XY:
74314
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
1019
AN:
3478
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
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at