chrX-120447885-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_002294.3(LAMP2):āc.697C>Gā(p.Leu233Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000892 in 112,160 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. Variant has been reported in ClinVar as Uncertain significance (ā ). Synonymous variant affecting the same amino acid position (i.e. L233L) has been classified as Likely benign.
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.697C>G | p.Leu233Val | missense_variant | 5/9 | ENST00000200639.9 | |
LAMP2 | NM_001122606.1 | c.697C>G | p.Leu233Val | missense_variant | 5/9 | ||
LAMP2 | NM_013995.2 | c.697C>G | p.Leu233Val | missense_variant | 5/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LAMP2 | ENST00000200639.9 | c.697C>G | p.Leu233Val | missense_variant | 5/9 | 1 | NM_002294.3 | P3 |
Frequencies
GnomAD3 genomes AF: 0.00000892 AC: 1AN: 112106Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34276
GnomAD3 exomes AF: 0.00000545 AC: 1AN: 183426Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 67868
GnomAD4 exome Cov.: 29
GnomAD4 genome AF: 0.00000892 AC: 1AN: 112160Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34340
ClinVar
Submissions by phenotype
Danon disease Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Aug 31, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at