rs200970855
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_001130987.2(DYSF):c.559G>A(p.Gly187Arg) variant causes a missense change. The variant allele was found at a frequency of 0.000281 in 1,613,876 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another nucleotide change resulting in same amino acid change has been previously reported as Uncertain significancein ClinVar. Synonymous variant affecting the same amino acid position (i.e. G187G) has been classified as Likely benign.
Frequency
Consequence
NM_001130987.2 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
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.559G>A | p.Gly187Arg | missense_variant | 7/56 | ENST00000410020.8 | |
DYSF | NM_003494.4 | c.463G>A | p.Gly155Arg | missense_variant | 6/55 | ENST00000258104.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DYSF | ENST00000410020.8 | c.559G>A | p.Gly187Arg | missense_variant | 7/56 | 1 | NM_001130987.2 | A1 | |
DYSF | ENST00000258104.8 | c.463G>A | p.Gly155Arg | missense_variant | 6/55 | 1 | NM_003494.4 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.000611 AC: 93AN: 152192Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000327 AC: 82AN: 250818Hom.: 2 AF XY: 0.000243 AC XY: 33AN XY: 135638
GnomAD4 exome AF: 0.000247 AC: 361AN: 1461566Hom.: 1 Cov.: 32 AF XY: 0.000237 AC XY: 172AN XY: 727056
GnomAD4 genome ? AF: 0.000611 AC: 93AN: 152310Hom.: 1 Cov.: 32 AF XY: 0.000765 AC XY: 57AN XY: 74472
ClinVar
Submissions by phenotype
not provided Uncertain:2Benign:1
Uncertain significance, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Oct 09, 2017 | - - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 09, 2020 | This variant is associated with the following publications: (PMID: 24838345, 26077850, 18853459, 25312915) - |
Uncertain significance, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Oct 18, 2023 | - - |
Autosomal recessive limb-girdle muscular dystrophy type 2B Benign:1
Benign, no assertion criteria provided | clinical testing | Natera, Inc. | Jan 23, 2020 | - - |
Qualitative or quantitative defects of dysferlin Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 30, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at