rs75713718
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_198271.5(LMOD3):āc.1257G>Cā(p.Met419Ile) variant causes a missense change. The variant allele was found at a frequency of 0.000677 in 1,613,846 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. M419T) has been classified as Uncertain significance.
Frequency
Consequence
NM_198271.5 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 | UniProt |
---|---|---|---|---|---|---|---|
LMOD3 | NM_198271.5 | c.1257G>C | p.Met419Ile | missense_variant | 2/3 | ENST00000420581.7 | |
LMOD3 | NM_001304418.3 | c.1257G>C | p.Met419Ile | missense_variant | 3/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LMOD3 | ENST00000420581.7 | c.1257G>C | p.Met419Ile | missense_variant | 2/3 | 1 | NM_198271.5 | P1 | |
LMOD3 | ENST00000475434.1 | c.1257G>C | p.Met419Ile | missense_variant | 3/4 | 5 | P1 | ||
LMOD3 | ENST00000489031.5 | c.1257G>C | p.Met419Ile | missense_variant | 3/4 | 2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00347 AC: 527AN: 152024Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000827 AC: 206AN: 249146Hom.: 1 AF XY: 0.000644 AC XY: 87AN XY: 135164
GnomAD4 exome AF: 0.000381 AC: 557AN: 1461704Hom.: 4 Cov.: 33 AF XY: 0.000338 AC XY: 246AN XY: 727132
GnomAD4 genome AF: 0.00352 AC: 536AN: 152142Hom.: 1 Cov.: 31 AF XY: 0.00348 AC XY: 259AN XY: 74392
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Mar 01, 2023 | LMOD3: BS1 - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 04, 2020 | - - |
Nemaline myopathy 10 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 30, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at