chr2-71574306-C-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001130987.2(DYSF):c.3337C>T(p.Arg1113Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00102 in 1,614,102 control chromosomes in the GnomAD database, including 16 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R1113G) has been classified as Uncertain significance.
Frequency
Consequence
NM_001130987.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DYSF | NM_001130987.2 | c.3337C>T | p.Arg1113Cys | missense_variant | 30/56 | ENST00000410020.8 | |
DYSF | NM_003494.4 | c.3283C>T | p.Arg1095Cys | missense_variant | 30/55 | ENST00000258104.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DYSF | ENST00000410020.8 | c.3337C>T | p.Arg1113Cys | missense_variant | 30/56 | 1 | NM_001130987.2 | A1 | |
DYSF | ENST00000258104.8 | c.3283C>T | p.Arg1095Cys | missense_variant | 30/55 | 1 | NM_003494.4 | A1 |
Frequencies
GnomAD3 genomes AF: 0.00551 AC: 839AN: 152230Hom.: 8 Cov.: 33
GnomAD3 exomes AF: 0.00147 AC: 368AN: 251190Hom.: 6 AF XY: 0.00113 AC XY: 153AN XY: 135770
GnomAD4 exome AF: 0.000553 AC: 809AN: 1461754Hom.: 8 Cov.: 33 AF XY: 0.000494 AC XY: 359AN XY: 727162
GnomAD4 genome AF: 0.00550 AC: 838AN: 152348Hom.: 8 Cov.: 33 AF XY: 0.00548 AC XY: 408AN XY: 74498
ClinVar
Submissions by phenotype
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | Dec 08, 2016 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Dec 16, 2013 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | May 11, 2018 | - - |
Autosomal recessive limb-girdle muscular dystrophy type 2B Benign:1
Likely benign, no assertion criteria provided | clinical testing | Natera, Inc. | Dec 04, 2019 | - - |
Qualitative or quantitative defects of dysferlin Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at