rs61738567
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001130987.2(DYSF):āc.4430A>Gā(p.Asp1477Gly) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00136 in 1,613,582 control chromosomes in the GnomAD database, including 27 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. D1477N) has been classified as Likely benign.
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.4430A>G | p.Asp1477Gly | missense_variant | 40/56 | ENST00000410020.8 | |
DYSF | NM_003494.4 | c.4376A>G | p.Asp1459Gly | missense_variant | 40/55 | ENST00000258104.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DYSF | ENST00000410020.8 | c.4430A>G | p.Asp1477Gly | missense_variant | 40/56 | 1 | NM_001130987.2 | A1 | |
DYSF | ENST00000258104.8 | c.4376A>G | p.Asp1459Gly | missense_variant | 40/55 | 1 | NM_003494.4 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.00721 AC: 1096AN: 152064Hom.: 13 Cov.: 33
GnomAD3 exomes AF: 0.00174 AC: 436AN: 250420Hom.: 3 AF XY: 0.00122 AC XY: 165AN XY: 135290
GnomAD4 exome AF: 0.000752 AC: 1099AN: 1461400Hom.: 14 Cov.: 32 AF XY: 0.000656 AC XY: 477AN XY: 726884
GnomAD4 genome ? AF: 0.00722 AC: 1099AN: 152182Hom.: 13 Cov.: 33 AF XY: 0.00702 AC XY: 522AN XY: 74392
ClinVar
Submissions by phenotype
not specified Benign:2
Likely benign, no assertion criteria provided | clinical testing | Genetic Services Laboratory, University of Chicago | - | Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated disease phenotype. NOT Sanger confirmed. - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 04, 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. - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jun 01, 2024 | DYSF: BS1, BS2 - |
Autosomal recessive limb-girdle muscular dystrophy type 2B Benign:1
Benign, no assertion criteria provided | clinical testing | Natera, Inc. | Sep 16, 2020 | - - |
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