3-69109097-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PM4
The NM_198271.5(LMOD3):āc.1681T>Cā(p.Ter561Glnext*?) variant causes a stop lost change. The variant allele was found at a frequency of 0.00000437 in 1,600,874 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 Uncertain significance (ā ).
Frequency
Consequence
NM_198271.5 stop_lost
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LMOD3 | ENST00000420581.7 | c.1681T>C | p.Ter561Glnext*? | stop_lost | Exon 3 of 3 | 1 | NM_198271.5 | ENSP00000414670.3 | ||
LMOD3 | ENST00000475434.1 | c.1681T>C | p.Ter561Glnext*? | stop_lost | Exon 4 of 4 | 5 | ENSP00000418645.1 | |||
LMOD3 | ENST00000489031.5 | c.1681T>C | p.Ter561Glnext*? | stop_lost | Exon 4 of 4 | 2 | ENSP00000417210.1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152182Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000887 AC: 2AN: 225416Hom.: 0 AF XY: 0.00000822 AC XY: 1AN XY: 121682
GnomAD4 exome AF: 0.00000414 AC: 6AN: 1448692Hom.: 0 Cov.: 29 AF XY: 0.00000278 AC XY: 2AN XY: 719122
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152182Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74344
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. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. ClinVar contains an entry for this variant (Variation ID: 1371723). This variant has not been reported in the literature in individuals affected with LMOD3-related conditions. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This sequence change disrupts the translational stop signal of the LMOD3 mRNA. It is expected to extend the length of the LMOD3 protein by 58 additional amino acid residues. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at