rs369607332
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 2P and 10B. PM2BP4BP6_Very_StrongBP7
The NM_001130987.2(DYSF):c.3166C>A(p.Arg1056=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000372 in 1,613,960 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 Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. R1056R) has been classified as Likely benign.
Frequency
Consequence
NM_001130987.2 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DYSF | NM_001130987.2 | c.3166C>A | p.Arg1056= | synonymous_variant | 29/56 | ENST00000410020.8 | |
DYSF | NM_003494.4 | c.3112C>A | p.Arg1038= | synonymous_variant | 29/55 | ENST00000258104.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DYSF | ENST00000410020.8 | c.3166C>A | p.Arg1056= | synonymous_variant | 29/56 | 1 | NM_001130987.2 | A1 | |
DYSF | ENST00000258104.8 | c.3112C>A | p.Arg1038= | synonymous_variant | 29/55 | 1 | NM_003494.4 | A1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152190Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000160 AC: 4AN: 250626Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135606
GnomAD4 exome AF: 0.00000342 AC: 5AN: 1461770Hom.: 0 Cov.: 32 AF XY: 0.00000550 AC XY: 4AN XY: 727204
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152190Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74338
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Aug 28, 2023 | - - |
Qualitative or quantitative defects of dysferlin Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 04, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at