9-110695519-A-G
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_005592.4(MUSK):āc.475A>Gā(p.Ser159Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.157 in 1,555,198 control chromosomes in the GnomAD database, including 20,579 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Consequence
NM_005592.4 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MUSK | NM_005592.4 | c.475A>G | p.Ser159Gly | missense_variant | 4/15 | ENST00000374448.9 | NP_005583.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MUSK | ENST00000374448.9 | c.475A>G | p.Ser159Gly | missense_variant | 4/15 | 5 | NM_005592.4 | ENSP00000363571.4 | ||
MUSK | ENST00000416899.7 | c.475A>G | p.Ser159Gly | missense_variant | 4/14 | 5 | ENSP00000393608.3 | |||
MUSK | ENST00000189978.10 | c.475A>G | p.Ser159Gly | missense_variant | 4/14 | 5 | ENSP00000189978.6 | |||
MUSK | ENST00000374439.1 | c.169A>G | p.Ser57Gly | missense_variant | 2/4 | 5 | ENSP00000363562.2 |
Frequencies
GnomAD3 genomes AF: 0.124 AC: 18932AN: 152156Hom.: 1528 Cov.: 32
GnomAD3 exomes AF: 0.148 AC: 26461AN: 178208Hom.: 2252 AF XY: 0.152 AC XY: 14303AN XY: 94378
GnomAD4 exome AF: 0.161 AC: 225809AN: 1402922Hom.: 19046 Cov.: 29 AF XY: 0.161 AC XY: 111801AN XY: 693436
GnomAD4 genome AF: 0.124 AC: 18941AN: 152276Hom.: 1533 Cov.: 32 AF XY: 0.128 AC XY: 9534AN XY: 74452
ClinVar
Submissions by phenotype
not specified Benign:3
Benign, criteria provided, single submitter | clinical testing | GeneDx | Feb 19, 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. - |
Benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Aug 15, 2013 | - - |
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
not provided Benign:1
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Fetal akinesia deformation sequence 1;C4225368:Congenital myasthenic syndrome 9 Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Feb 01, 2024 | - - |
Congenital myasthenic syndrome 9 Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 12, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at