9-110800369-A-G
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_005592.4(MUSK):c.1991A>G(p.Asn664Ser) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.011 in 1,613,820 control chromosomes in the GnomAD database, including 162 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
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
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MUSK | ENST00000374448.9 | c.1991A>G | p.Asn664Ser | missense_variant | Exon 15 of 15 | 5 | NM_005592.4 | ENSP00000363571.4 | ||
MUSK | ENST00000416899.7 | c.1967A>G | p.Asn656Ser | missense_variant | Exon 14 of 14 | 5 | ENSP00000393608.3 | |||
MUSK | ENST00000189978.10 | c.1733A>G | p.Asn578Ser | missense_variant | Exon 14 of 14 | 5 | ENSP00000189978.6 |
Frequencies
GnomAD3 genomes AF: 0.00811 AC: 1232AN: 151996Hom.: 13 Cov.: 32
GnomAD3 exomes AF: 0.00833 AC: 2076AN: 249104Hom.: 14 AF XY: 0.00867 AC XY: 1171AN XY: 135108
GnomAD4 exome AF: 0.0113 AC: 16491AN: 1461706Hom.: 149 Cov.: 32 AF XY: 0.0112 AC XY: 8165AN XY: 727134
GnomAD4 genome AF: 0.00809 AC: 1231AN: 152114Hom.: 13 Cov.: 32 AF XY: 0.00745 AC XY: 554AN XY: 74378
ClinVar
Submissions by phenotype
not specified Benign:2
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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:2
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MUSK: BS1, BS2 -
Fetal akinesia deformation sequence 1;C4225368:Congenital myasthenic syndrome 9 Benign:2
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Congenital myasthenic syndrome 9 Benign:1
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). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to rule this variant out of causing disease. Therefore, this variant is classified as benign. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at