rs765143363
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 0P and 1B. BP4
The NM_013995.2(LAMP2):c.1106C>T(p.Ser369Leu) variant causes a missense change. The variant allele was found at a frequency of 0.00000747 in 1,205,274 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 1 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_013995.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LAMP2 | NM_002294.3 | c.1093+2449C>T | intron_variant | Intron 8 of 8 | ENST00000200639.9 | NP_002285.1 | ||
LAMP2 | NM_013995.2 | c.1106C>T | p.Ser369Leu | missense_variant | Exon 9 of 9 | NP_054701.1 | ||
LAMP2 | NM_001122606.1 | c.1093+2449C>T | intron_variant | Intron 8 of 8 | NP_001116078.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000896 AC: 1AN: 111617Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 33813
GnomAD3 exomes AF: 0.0000218 AC: 4AN: 183175Hom.: 0 AF XY: 0.0000148 AC XY: 1AN XY: 67697
GnomAD4 exome AF: 0.00000731 AC: 8AN: 1093657Hom.: 0 Cov.: 28 AF XY: 0.00000278 AC XY: 1AN XY: 359169
GnomAD4 genome AF: 0.00000896 AC: 1AN: 111617Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 33813
ClinVar
Submissions by phenotype
not specified Uncertain:1
The p.Ser369Leu variant in LAMP2 has not been previously reported in individuals with cardiomyopathy, but has been identified in 2/47977 European chromosomes, i ncluding one hemizygote, by the Exome Aggregation Consortium (ExAC, http://exac. broadinstitute.org; dbSNP rs765143363). Computational prediction tools and conse rvation analysis suggest that the p.Ser369Leu variant may not impact the protein . Although this information is not predictive enough to rule out pathogenicity m issense variants in this gene are typically not pathogenic. In summary, the clin ical significance of the p.Ser369Leu variant is uncertain. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at