rs150380359
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 2P and 9B. PM2BP4_StrongBP6BS1
The NM_198271.5(LMOD3):āc.416A>Gā(p.Asn139Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000222 in 1,564,196 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. N139N) has been classified as Likely benign.
Frequency
Consequence
NM_198271.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LMOD3 | NM_198271.5 | c.416A>G | p.Asn139Ser | missense_variant | 2/3 | ENST00000420581.7 | |
LMOD3 | NM_001304418.3 | c.416A>G | p.Asn139Ser | missense_variant | 3/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LMOD3 | ENST00000420581.7 | c.416A>G | p.Asn139Ser | missense_variant | 2/3 | 1 | NM_198271.5 | P1 | |
LMOD3 | ENST00000475434.1 | c.416A>G | p.Asn139Ser | missense_variant | 3/4 | 5 | P1 | ||
LMOD3 | ENST00000489031.5 | c.416A>G | p.Asn139Ser | missense_variant | 3/4 | 2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000460 AC: 70AN: 152190Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000226 AC: 40AN: 176928Hom.: 0 AF XY: 0.000159 AC XY: 15AN XY: 94104
GnomAD4 exome AF: 0.000194 AC: 274AN: 1411888Hom.: 0 Cov.: 31 AF XY: 0.000195 AC XY: 136AN XY: 698078
GnomAD4 genome AF: 0.000479 AC: 73AN: 152308Hom.: 0 Cov.: 31 AF XY: 0.000322 AC XY: 24AN XY: 74494
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 09, 2021 | The c.416A>G (p.N139S) alteration is located in exon 2 (coding exon 2) of the LMOD3 gene. This alteration results from a A to G substitution at nucleotide position 416, causing the asparagine (N) at amino acid position 139 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Nemaline myopathy 10 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 18, 2024 | - - |
LMOD3-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Mar 07, 2023 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at