rs727504953
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_002294.3(LAMP2):c.277G>C(p.Gly93Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 12/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Uncertain significancein ClinVar.
Frequency
Consequence
NM_002294.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LAMP2 | NM_002294.3 | c.277G>C | p.Gly93Arg | missense_variant | 3/9 | ENST00000200639.9 | |
LAMP2 | NM_001122606.1 | c.277G>C | p.Gly93Arg | missense_variant | 3/9 | ||
LAMP2 | NM_013995.2 | c.277G>C | p.Gly93Arg | missense_variant | 3/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LAMP2 | ENST00000200639.9 | c.277G>C | p.Gly93Arg | missense_variant | 3/9 | 1 | NM_002294.3 | P3 | |
LAMP2 | ENST00000434600.6 | c.277G>C | p.Gly93Arg | missense_variant | 3/9 | 1 | A1 | ||
LAMP2 | ENST00000371335.4 | c.277G>C | p.Gly93Arg | missense_variant | 3/9 | 1 | A1 | ||
LAMP2 | ENST00000706600.1 | c.277G>C | p.Gly93Arg | missense_variant | 3/9 |
Frequencies
GnomAD3 genomes ? Cov.: 21
GnomAD3 exomes AF: 0.00000545 AC: 1AN: 183481Hom.: 0 AF XY: 0.0000147 AC XY: 1AN XY: 67925
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000182 AC: 2AN: 1096487Hom.: 0 Cov.: 30 AF XY: 0.00000553 AC XY: 2AN XY: 361861
GnomAD4 genome ? Cov.: 21
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at