rs758495000
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PM4_Supporting
The NM_000426.4(LAMA2):c.6201_6203delGAA(p.Lys2067del) variant causes a disruptive inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000248 in 1,613,968 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Consequence
NM_000426.4 disruptive_inframe_deletion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LAMA2 | NM_000426.4 | c.6201_6203delGAA | p.Lys2067del | disruptive_inframe_deletion | Exon 43 of 65 | ENST00000421865.3 | NP_000417.3 | |
LAMA2 | NM_001079823.2 | c.6201_6203delGAA | p.Lys2067del | disruptive_inframe_deletion | Exon 43 of 64 | NP_001073291.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LAMA2 | ENST00000421865.3 | c.6201_6203delGAA | p.Lys2067del | disruptive_inframe_deletion | Exon 43 of 65 | 5 | NM_000426.4 | ENSP00000400365.2 | ||
LAMA2 | ENST00000618192.5 | c.6465_6467delGAA | p.Lys2155del | disruptive_inframe_deletion | Exon 44 of 66 | 5 | ENSP00000480802.2 | |||
LAMA2 | ENST00000617695.5 | c.6201_6203delGAA | p.Lys2067del | disruptive_inframe_deletion | Exon 43 of 64 | 5 | ENSP00000481744.2 | |||
ENSG00000226149 | ENST00000665046.1 | n.1301_1303delTTC | non_coding_transcript_exon_variant | Exon 10 of 10 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152200Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00000399 AC: 1AN: 250800Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135522
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461650Hom.: 0 AF XY: 0.00000275 AC XY: 2AN XY: 727138
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152318Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74486
ClinVar
Submissions by phenotype
Merosin deficient congenital muscular dystrophy Uncertain:1
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LAMA2-related muscular dystrophy Uncertain:1
This variant, c.6201_6203del, results in the deletion of 1 amino acid(s) of the LAMA2 protein (p.Lys2067del), but otherwise preserves the integrity of the reading frame. This variant is present in population databases (rs758495000, gnomAD 0.007%). This variant has not been reported in the literature in individuals affected with LAMA2-related conditions. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant 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. -
not provided Uncertain:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at