9-110785683-C-A
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 2P and 13B. PM2BP4_StrongBP6_Very_StrongBP7
The NM_005592.4(MUSK):c.1743C>A(p.Ile581=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000653 in 1,607,022 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. I581I) has been classified as Likely benign.
Frequency
Consequence
NM_005592.4 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 |
---|---|---|---|---|---|---|---|
MUSK | NM_005592.4 | c.1743C>A | p.Ile581= | synonymous_variant | 13/15 | ENST00000374448.9 | |
LOC107987115 | XR_001746892.2 | n.9G>T | non_coding_transcript_exon_variant | 1/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MUSK | ENST00000374448.9 | c.1743C>A | p.Ile581= | synonymous_variant | 13/15 | 5 | NM_005592.4 | P4 | |
MUSK | ENST00000416899.7 | c.1719C>A | p.Ile573= | synonymous_variant | 12/14 | 5 | A1 | ||
MUSK | ENST00000189978.10 | c.1485C>A | p.Ile495= | synonymous_variant | 12/14 | 5 | |||
MUSK | ENST00000374438.1 | n.774C>A | non_coding_transcript_exon_variant | 2/3 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000725 AC: 11AN: 151688Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000729 AC: 18AN: 247038Hom.: 0 AF XY: 0.0000597 AC XY: 8AN XY: 134062
GnomAD4 exome AF: 0.0000646 AC: 94AN: 1455334Hom.: 0 Cov.: 31 AF XY: 0.0000649 AC XY: 47AN XY: 723786
GnomAD4 genome AF: 0.0000725 AC: 11AN: 151688Hom.: 0 Cov.: 31 AF XY: 0.0000540 AC XY: 4AN XY: 74046
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Fetal akinesia deformation sequence 1;C4225368:Congenital myasthenic syndrome 9 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 05, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at