3-69109096-T-TA
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PM4
The NM_198271.5(LMOD3):c.1681dupT(p.Ter561LeufsTer8) variant causes a frameshift, stop lost change. The variant allele was found at a frequency of 0.00000207 in 1,448,518 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_198271.5 frameshift, stop_lost
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LMOD3 | NM_198271.5 | c.1681dupT | p.Ter561LeufsTer8 | frameshift_variant, stop_lost | Exon 3 of 3 | ENST00000420581.7 | NP_938012.2 | |
LMOD3 | NM_001304418.3 | c.1681dupT | p.Ter561LeufsTer8 | frameshift_variant, stop_lost | Exon 4 of 4 | NP_001291347.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LMOD3 | ENST00000420581.7 | c.1681dupT | p.Ter561LeufsTer8 | frameshift_variant, stop_lost | Exon 3 of 3 | 1 | NM_198271.5 | ENSP00000414670.3 | ||
LMOD3 | ENST00000475434.1 | c.1681dupT | p.Ter561LeufsTer8 | frameshift_variant, stop_lost | Exon 4 of 4 | 5 | ENSP00000418645.1 | |||
LMOD3 | ENST00000489031.5 | c.1681dupT | p.Ter561LeufsTer8 | frameshift_variant, stop_lost | Exon 4 of 4 | 2 | ENSP00000417210.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 0.00000207 AC: 3AN: 1448518Hom.: 0 Cov.: 29 AF XY: 0.00000417 AC XY: 3AN XY: 719032
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Nemaline myopathy 10 Uncertain:1
In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. This variant has not been reported in the literature in individuals with LMOD3-related disease. This variant is not present in population databases (ExAC no frequency). This sequence change disrupts the translational stop signal of the LMOD3 mRNA. It is expected to extend the length of the LMOD3 protein by 7 additional amino acid residues. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at