chr3-69109111-G-T
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The NM_198271.5(LMOD3):c.1667C>A(p.Pro556Gln) variant causes a missense change. The variant allele was found at a frequency of 0.000711 in 1,602,286 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P556R) 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 -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LMOD3 | NM_198271.5 | c.1667C>A | p.Pro556Gln | missense_variant | 3/3 | ENST00000420581.7 | |
LMOD3 | NM_001304418.3 | c.1667C>A | p.Pro556Gln | missense_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LMOD3 | ENST00000420581.7 | c.1667C>A | p.Pro556Gln | missense_variant | 3/3 | 1 | NM_198271.5 | P1 | |
LMOD3 | ENST00000475434.1 | c.1667C>A | p.Pro556Gln | missense_variant | 4/4 | 5 | P1 | ||
LMOD3 | ENST00000489031.5 | c.1667C>A | p.Pro556Gln | missense_variant | 4/4 | 2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000487 AC: 74AN: 151990Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00110 AC: 251AN: 227842Hom.: 0 AF XY: 0.00138 AC XY: 170AN XY: 123072
GnomAD4 exome AF: 0.000736 AC: 1067AN: 1450178Hom.: 6 Cov.: 29 AF XY: 0.000928 AC XY: 668AN XY: 720012
GnomAD4 genome AF: 0.000480 AC: 73AN: 152108Hom.: 0 Cov.: 31 AF XY: 0.000592 AC XY: 44AN XY: 74318
ClinVar
Submissions by phenotype
Nemaline myopathy 10 Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 22, 2023 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Dec 29, 2023 | - - |
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genomic Diagnostic Laboratory, Division of Genomic Diagnostics, Children's Hospital of Philadelphia | Apr 12, 2015 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Dec 01, 2022 | LMOD3: BS1 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at