rs2820312
Variant summary
Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1
The NM_012134.3(LMOD1):c.884C>T(p.Thr295Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.311 in 1,613,506 control chromosomes in the GnomAD database, including 80,997 homozygotes. In-silico tool predicts a benign outcome for this variant. 16/22 in silico tools predict a benign outcome for this variant. Variant has been reported in Lovd as Benign (no stars). Another nucleotide change resulting in the same amino acid substitution has been previously reported as Likely benign in UniProt. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T295S) has been classified as Uncertain significance.
Frequency
Consequence
NM_012134.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Our verdict: Benign. The variant received -13 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LMOD1 | ENST00000367288.5 | c.884C>T | p.Thr295Met | missense_variant | Exon 2 of 3 | 1 | NM_012134.3 | ENSP00000356257.4 | ||
ENSG00000223774 | ENST00000414927.5 | n.*151G>A | downstream_gene_variant | 3 | ||||||
ENSG00000223774 | ENST00000458139.1 | n.*151G>A | downstream_gene_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.277 AC: 42009AN: 151862Hom.: 6062 Cov.: 31 show subpopulations
GnomAD2 exomes AF: 0.278 AC: 69145AN: 248924 AF XY: 0.280 show subpopulations
GnomAD4 exome AF: 0.314 AC: 459377AN: 1461524Hom.: 74932 Cov.: 57 AF XY: 0.313 AC XY: 227470AN XY: 727054 show subpopulations
GnomAD4 genome AF: 0.277 AC: 42025AN: 151982Hom.: 6065 Cov.: 31 AF XY: 0.274 AC XY: 20382AN XY: 74298 show subpopulations
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at