2-71453820-C-T
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_003494.4(DYSF):c.-179C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000191 in 522,328 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000019 ( 0 hom. )
Consequence
DYSF
NM_003494.4 5_prime_UTR
NM_003494.4 5_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.122
Publications
0 publications found
Genes affected
DYSF (HGNC:3097): (dysferlin) The protein encoded by this gene belongs to the ferlin family and is a skeletal muscle protein found associated with the sarcolemma. It is involved in muscle contraction and contains C2 domains that play a role in calcium-mediated membrane fusion events, suggesting that it may be involved in membrane regeneration and repair. In addition, the protein encoded by this gene binds caveolin-3, a skeletal muscle membrane protein which is important in the formation of caveolae. Specific mutations in this gene have been shown to cause autosomal recessive limb girdle muscular dystrophy type 2B (LGMD2B) as well as Miyoshi myopathy. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2008]
DYSF Gene-Disease associations (from GenCC):
- autosomal recessive limb-girdle muscular dystrophyInheritance: AR Classification: DEFINITIVE Submitted by: ClinGen
- neuromuscular disease caused by qualitative or quantitative defects of dysferlinInheritance: AR Classification: DEFINITIVE Submitted by: Myriad Women’s Health
- autosomal recessive limb-girdle muscular dystrophy type 2BInheritance: AR Classification: STRONG, SUPPORTIVE Submitted by: Orphanet, Labcorp Genetics (formerly Invitae)
- distal myopathy with anterior tibial onsetInheritance: AR Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
- congenital myopathy, Paradas typeInheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
- Miyoshi myopathyInheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
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ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.59).
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD4 exome AF: 0.00000191 AC: 1AN: 522328Hom.: 0 Cov.: 6 AF XY: 0.00000360 AC XY: 1AN XY: 278062 show subpopulations
GnomAD4 exome
AF:
AC:
1
AN:
522328
Hom.:
Cov.:
6
AF XY:
AC XY:
1
AN XY:
278062
show subpopulations
African (AFR)
AF:
AC:
0
AN:
14896
American (AMR)
AF:
AC:
0
AN:
30868
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
17106
East Asian (EAS)
AF:
AC:
0
AN:
31336
South Asian (SAS)
AF:
AC:
0
AN:
56060
European-Finnish (FIN)
AF:
AC:
0
AN:
32698
Middle Eastern (MID)
AF:
AC:
0
AN:
2358
European-Non Finnish (NFE)
AF:
AC:
1
AN:
308294
Other (OTH)
AF:
AC:
0
AN:
28712
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.625
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.:
32
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
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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