rs116426399
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 2P and 12B. PM2BP4_StrongBP6_Very_Strong
The NM_001130987.2(DYSF):c.3968C>A(p.Thr1323Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000346 in 1,613,568 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_001130987.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DYSF | NM_001130987.2 | c.3968C>A | p.Thr1323Lys | missense_variant | 37/56 | ENST00000410020.8 | |
DYSF | NM_003494.4 | c.3914C>A | p.Thr1305Lys | missense_variant | 37/55 | ENST00000258104.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DYSF | ENST00000410020.8 | c.3968C>A | p.Thr1323Lys | missense_variant | 37/56 | 1 | NM_001130987.2 | A1 | |
DYSF | ENST00000258104.8 | c.3914C>A | p.Thr1305Lys | missense_variant | 37/55 | 1 | NM_003494.4 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.00187 AC: 284AN: 152226Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000442 AC: 111AN: 250914Hom.: 0 AF XY: 0.000347 AC XY: 47AN XY: 135610
GnomAD4 exome AF: 0.000187 AC: 273AN: 1461224Hom.: 0 Cov.: 31 AF XY: 0.000180 AC XY: 131AN XY: 726942
GnomAD4 genome ? AF: 0.00187 AC: 285AN: 152344Hom.: 0 Cov.: 32 AF XY: 0.00165 AC XY: 123AN XY: 74498
ClinVar
Submissions by phenotype
not provided Benign:3
Likely benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | May 03, 2019 | - - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 08, 2019 | - - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Sep 01, 2020 | - - |
Qualitative or quantitative defects of dysferlin Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Apr 27, 2017 | This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Jul 01, 2016 | - - |
DYSF-related condition Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Dec 18, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at