2-219418461-C-T
Variant names:
Variant summary
Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001927.4(DES):c.-2C>T variant causes a 5 prime UTR change. The variant allele was found at a frequency of 0.000000696 in 1,437,348 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (no stars).
Frequency
Genomes: not found (cov: 33)
Exomes 𝑓: 7.0e-7 ( 0 hom. )
Consequence
DES
NM_001927.4 5_prime_UTR
NM_001927.4 5_prime_UTR
Scores
1
1
Clinical Significance
Conservation
PhyloP100: 4.56
Publications
0 publications found
Genes affected
DES (HGNC:2770): (desmin) This gene encodes a muscle-specific class III intermediate filament. Homopolymers of this protein form a stable intracytoplasmic filamentous network connecting myofibrils to each other and to the plasma membrane. Mutations in this gene are associated with desmin-related myopathy, a familial cardiac and skeletal myopathy (CSM), and with distal myopathies. [provided by RefSeq, Jul 2008]
DES Gene-Disease associations (from GenCC):
- dilated cardiomyopathyInheritance: AD Classification: DEFINITIVE Submitted by: ClinGen
- dilated cardiomyopathy 1IInheritance: AD Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), G2P, Ambry Genetics
- myofibrillar myopathy 1Inheritance: AD, AR, SD Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), G2P, Ambry Genetics
- atrioventricular blockInheritance: AD, AR Classification: STRONG Submitted by: Genomics England PanelApp
- arrhythmogenic right ventricular cardiomyopathyInheritance: AD Classification: MODERATE Submitted by: ClinGen
- familial isolated dilated cardiomyopathyInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- neurogenic scapuloperoneal syndrome, Kaeser typeInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 0 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.3).
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
33
GnomAD4 exome AF: 6.96e-7 AC: 1AN: 1437348Hom.: 0 Cov.: 29 AF XY: 0.00000140 AC XY: 1AN XY: 715146 show subpopulations
GnomAD4 exome
AF:
AC:
1
AN:
1437348
Hom.:
Cov.:
29
AF XY:
AC XY:
1
AN XY:
715146
show subpopulations
African (AFR)
AF:
AC:
0
AN:
31408
American (AMR)
AF:
AC:
0
AN:
43804
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
25582
East Asian (EAS)
AF:
AC:
0
AN:
38034
South Asian (SAS)
AF:
AC:
0
AN:
84530
European-Finnish (FIN)
AF:
AC:
0
AN:
42950
Middle Eastern (MID)
AF:
AC:
0
AN:
4648
European-Non Finnish (NFE)
AF:
AC:
1
AN:
1106862
Other (OTH)
AF:
AC:
0
AN:
59530
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.525
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
GnomAD4 genome
Cov.:
33
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Cardiomyopathy Uncertain:1
-
Institute of Human Genetics, University of Wuerzburg
Significance:Uncertain significance
Review Status:no assertion criteria provided
Collection Method:clinical testing
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Uncertain
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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