NM_013451.4:c.88+1005C>A
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_013451.4(MYOF):c.88+1005C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.777 in 152,108 control chromosomes in the GnomAD database, including 46,337 homozygotes. 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: 𝑓 0.78 ( 46337 hom., cov: 32)
Consequence
MYOF
NM_013451.4 intron
NM_013451.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.487
Publications
1 publications found
Genes affected
MYOF (HGNC:3656): (myoferlin) Mutations in dysferlin, a protein associated with the plasma membrane, can cause muscle weakness that affects both proximal and distal muscles. The protein encoded by this gene is a type II membrane protein that is structurally similar to dysferlin. It is a member of the ferlin family and associates with both plasma and nuclear membranes. The protein contains C2 domains that play a role in calcium-mediated membrane fusion events, suggesting that it may be involved in membrane regeneration and repair. Two transcript variants encoding different isoforms have been found for this gene. Other possible variants have been detected, but their full-length nature has not been determined. [provided by RefSeq, Dec 2008]
MYOF Gene-Disease associations (from GenCC):
- angioedema, hereditary, 7Inheritance: Unknown Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae)
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ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.834 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.777 AC: 118047AN: 151990Hom.: 46297 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
118047
AN:
151990
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:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.777 AC: 118143AN: 152108Hom.: 46337 Cov.: 32 AF XY: 0.773 AC XY: 57452AN XY: 74348 show subpopulations
GnomAD4 genome
AF:
AC:
118143
AN:
152108
Hom.:
Cov.:
32
AF XY:
AC XY:
57452
AN XY:
74348
show subpopulations
African (AFR)
AF:
AC:
29039
AN:
41450
American (AMR)
AF:
AC:
12046
AN:
15286
Ashkenazi Jewish (ASJ)
AF:
AC:
2704
AN:
3472
East Asian (EAS)
AF:
AC:
2479
AN:
5162
South Asian (SAS)
AF:
AC:
4074
AN:
4828
European-Finnish (FIN)
AF:
AC:
8089
AN:
10592
Middle Eastern (MID)
AF:
AC:
231
AN:
294
European-Non Finnish (NFE)
AF:
AC:
57087
AN:
67996
Other (OTH)
AF:
AC:
1641
AN:
2116
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.504
Heterozygous variant carriers
0
1302
2604
3907
5209
6511
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
866
1732
2598
3464
4330
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
2345
AN:
3478
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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