NM_001161403.3:c.958_969dupCTGAAGAAGCTG
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM4BS2
The NM_001161403.3(LIMS2):c.958_969dupCTGAAGAAGCTG(p.Leu323_Ser324insLeuLysLysLeu) variant causes a conservative inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000192 in 1,613,816 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Consequence
NM_001161403.3 conservative_inframe_insertion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152130Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000915 AC: 23AN: 251296Hom.: 0 AF XY: 0.0000810 AC XY: 11AN XY: 135822
GnomAD4 exome AF: 0.0000185 AC: 27AN: 1461686Hom.: 0 Cov.: 32 AF XY: 0.0000193 AC XY: 14AN XY: 727160
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152130Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74322
ClinVar
Submissions by phenotype
Autosomal recessive limb-girdle muscular dystrophy type 2W Uncertain:2
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The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the ExAC database. This variant has not been reported in the literature in individuals with LIMS2-related disease. ClinVar contains an entry for this variant (Variation ID: 475543). Experimental studies and prediction algorithms are not available for this variant, and the functional significance of the affected amino acid(s) is currently unknown. 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. This variant, c.1030_1041dupCTGAAGAAGCTG, results in the insertion of 4 amino acid(s) to the LIMS2 protein (p.Leu344_Leu347dup), but otherwise preserves the integrity of the reading frame. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at