rs7441
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_ModerateBP6_ModerateBA1
The NM_001920.5(DCN):c.*160C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0766 in 630,010 control chromosomes in the GnomAD database, including 2,294 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.097 ( 945 hom., cov: 32)
Exomes 𝑓: 0.070 ( 1349 hom. )
Consequence
DCN
NM_001920.5 3_prime_UTR
NM_001920.5 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 2.52
Genes affected
DCN (HGNC:2705): (decorin) This gene encodes a member of the small leucine-rich proteoglycan family of proteins. Alternative splicing results in multiple transcript variants, at least one of which encodes a preproprotein that is proteolytically processed to generate the mature protein. This protein plays a role in collagen fibril assembly. Binding of this protein to multiple cell surface receptors mediates its role in tumor suppression, including a stimulatory effect on autophagy and inflammation and an inhibitory effect on angiogenesis and tumorigenesis. This gene and the related gene biglycan are thought to be the result of a gene duplication. Mutations in this gene are associated with congenital stromal corneal dystrophy in human patients. [provided by RefSeq, Nov 2015]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.34).
BP6
?
Variant 12-91145898-G-A is Benign according to our data. Variant chr12-91145898-G-A is described in ClinVar as [Benign]. Clinvar id is 310647.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr12-91145898-G-A is described in Lovd as [Benign].
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.17 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DCN | NM_001920.5 | c.*160C>T | 3_prime_UTR_variant | 8/8 | ENST00000052754.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DCN | ENST00000052754.10 | c.*160C>T | 3_prime_UTR_variant | 8/8 | 1 | NM_001920.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0966 AC: 14689AN: 152080Hom.: 943 Cov.: 32
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GnomAD4 exome AF: 0.0702 AC: 33522AN: 477812Hom.: 1349 Cov.: 5 AF XY: 0.0687 AC XY: 17495AN XY: 254694
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GnomAD4 genome ? AF: 0.0967 AC: 14711AN: 152198Hom.: 945 Cov.: 32 AF XY: 0.0935 AC XY: 6959AN XY: 74408
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Congenital stromal corneal dystrophy 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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BayesDel_noAF
Benign
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