rs886043009
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6BP7
The NM_001130987.2(DYSF):c.397C>T(p.Leu133=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000516 in 1,551,620 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 Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. L133L) has been classified as Likely benign.
Frequency
Consequence
NM_001130987.2 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DYSF | NM_001130987.2 | c.397C>T | p.Leu133= | synonymous_variant | 5/56 | ENST00000410020.8 | |
DYSF | NM_003494.4 | c.394C>T | p.Leu132= | synonymous_variant | 5/55 | ENST00000258104.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DYSF | ENST00000410020.8 | c.397C>T | p.Leu133= | synonymous_variant | 5/56 | 1 | NM_001130987.2 | A1 | |
DYSF | ENST00000258104.8 | c.394C>T | p.Leu132= | synonymous_variant | 5/55 | 1 | NM_003494.4 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152232Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000128 AC: 2AN: 156834Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 82532
GnomAD4 exome AF: 0.00000286 AC: 4AN: 1399388Hom.: 0 Cov.: 32 AF XY: 0.00000145 AC XY: 1AN XY: 690198
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152232Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74376
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Nov 30, 2015 | - - |
Qualitative or quantitative defects of dysferlin Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 24, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at