rs727503122
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_002294.3(LAMP2):c.42C>T(p.Leu14=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000014 in 1,210,847 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 7 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. L14L) has been classified as Likely benign.
Frequency
Consequence
NM_002294.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -17 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LAMP2 | NM_002294.3 | c.42C>T | p.Leu14= | synonymous_variant | 1/9 | ENST00000200639.9 | |
LAMP2 | NM_001122606.1 | c.42C>T | p.Leu14= | synonymous_variant | 1/9 | ||
LAMP2 | NM_013995.2 | c.42C>T | p.Leu14= | synonymous_variant | 1/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LAMP2 | ENST00000200639.9 | c.42C>T | p.Leu14= | synonymous_variant | 1/9 | 1 | NM_002294.3 | P3 | |
LAMP2 | ENST00000434600.6 | c.42C>T | p.Leu14= | synonymous_variant | 1/9 | 1 | A1 | ||
LAMP2 | ENST00000371335.4 | c.42C>T | p.Leu14= | synonymous_variant | 1/9 | 1 | A1 | ||
LAMP2 | ENST00000706600.1 | c.42C>T | p.Leu14= | synonymous_variant | 1/9 |
Frequencies
GnomAD3 genomes ? AF: 0.0000532 AC: 6AN: 112807Hom.: 0 Cov.: 23 AF XY: 0.0000858 AC XY: 3AN XY: 34955
GnomAD3 exomes AF: 0.0000274 AC: 5AN: 182198Hom.: 0 AF XY: 0.0000149 AC XY: 1AN XY: 67294
GnomAD4 exome AF: 0.0000100 AC: 11AN: 1098040Hom.: 0 Cov.: 30 AF XY: 0.0000110 AC XY: 4AN XY: 363434
GnomAD4 genome ? AF: 0.0000532 AC: 6AN: 112807Hom.: 0 Cov.: 23 AF XY: 0.0000858 AC XY: 3AN XY: 34955
ClinVar
Submissions by phenotype
not specified Benign:2
Benign, no assertion criteria provided | clinical testing | Clinical Genetics, Academic Medical Center | - | - - |
Likely benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Jun 13, 2014 | Leu14Leu in exon 1 of LAMP2: This variant is not expected to have clinical signi ficance because it does not alter an amino acid residue and is not located withi n the splice consensus sequence. - |
not provided Benign:2
Likely benign, no assertion criteria provided | clinical testing | Genome Diagnostics Laboratory, University Medical Center Utrecht | - | - - |
Likely benign, no assertion criteria provided | clinical testing | Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ | - | - - |
Danon disease Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 20, 2024 | - - |
Cardiovascular phenotype Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 24, 2019 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at