rs377235191
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 2P and 13B. PM2BP4_StrongBP6_Very_StrongBP7
The NM_001130987.2(DYSF):c.3126G>A(p.Pro1042=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000651 in 1,614,076 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. P1042P) 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 -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DYSF | NM_001130987.2 | c.3126G>A | p.Pro1042= | synonymous_variant | 29/56 | ENST00000410020.8 | |
DYSF | NM_003494.4 | c.3072G>A | p.Pro1024= | synonymous_variant | 29/55 | ENST00000258104.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DYSF | ENST00000410020.8 | c.3126G>A | p.Pro1042= | synonymous_variant | 29/56 | 1 | NM_001130987.2 | A1 | |
DYSF | ENST00000258104.8 | c.3072G>A | p.Pro1024= | synonymous_variant | 29/55 | 1 | NM_003494.4 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000329 AC: 5AN: 152204Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000399 AC: 10AN: 250598Hom.: 0 AF XY: 0.0000516 AC XY: 7AN XY: 135598
GnomAD4 exome AF: 0.0000677 AC: 99AN: 1461754Hom.: 0 Cov.: 32 AF XY: 0.0000564 AC XY: 41AN XY: 727174
GnomAD4 genome ? AF: 0.0000394 AC: 6AN: 152322Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74480
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Dec 28, 2017 | 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. - |
Qualitative or quantitative defects of dysferlin Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 21, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at