chr12-65169598-T-TGGC
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 1P and 5B. PM4_SupportingBS1_SupportingBS2
The NM_014319.5(LEMD3):c.9_11dupGGC(p.Ala4dup) variant causes a disruptive inframe insertion change. The variant allele was found at a frequency of 0.0000202 in 1,587,568 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_014319.5 disruptive_inframe_insertion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LEMD3 | NM_014319.5 | c.9_11dupGGC | p.Ala4dup | disruptive_inframe_insertion | Exon 1 of 13 | ENST00000308330.3 | NP_055134.2 | |
LEMD3 | NM_001167614.2 | c.9_11dupGGC | p.Ala4dup | disruptive_inframe_insertion | Exon 1 of 13 | NP_001161086.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 151996Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000147 AC: 3AN: 204058Hom.: 0 AF XY: 0.0000269 AC XY: 3AN XY: 111400
GnomAD4 exome AF: 0.0000209 AC: 30AN: 1435572Hom.: 0 Cov.: 32 AF XY: 0.0000253 AC XY: 18AN XY: 711742
GnomAD4 genome AF: 0.0000132 AC: 2AN: 151996Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74214
ClinVar
Submissions by phenotype
not provided 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. This variant has not been reported in the literature in individuals affected with LEMD3-related conditions. This variant is present in population databases (rs759986057, gnomAD 0.01%). This variant, c.9_11dup, results in the insertion of 1 amino acid(s) of the LEMD3 protein (p.Ala6dup), but otherwise preserves the integrity of the reading frame. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at