rs201209341
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The ENST00000200639.9(LAMP2):c.-10C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000752 in 1,210,116 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 32 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
ENST00000200639.9 5_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LAMP2 | NM_002294.3 | c.-10C>T | 5_prime_UTR_variant | 1/9 | ENST00000200639.9 | NP_002285.1 | ||
LAMP2 | NM_001122606.1 | c.-10C>T | 5_prime_UTR_variant | 1/9 | NP_001116078.1 | |||
LAMP2 | NM_013995.2 | c.-10C>T | 5_prime_UTR_variant | 1/9 | NP_054701.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LAMP2 | ENST00000200639.9 | c.-10C>T | 5_prime_UTR_variant | 1/9 | 1 | NM_002294.3 | ENSP00000200639 | P3 | ||
LAMP2 | ENST00000371335.4 | c.-10C>T | 5_prime_UTR_variant | 1/9 | 1 | ENSP00000360386 | A1 | |||
LAMP2 | ENST00000434600.6 | c.-10C>T | 5_prime_UTR_variant | 1/9 | 1 | ENSP00000408411 | A1 | |||
LAMP2 | ENST00000706600.1 | c.-10C>T | 5_prime_UTR_variant | 1/9 | ENSP00000516464 |
Frequencies
GnomAD3 genomes AF: 0.000267 AC: 30AN: 112485Hom.: 0 Cov.: 23 AF XY: 0.000433 AC XY: 15AN XY: 34631
GnomAD3 exomes AF: 0.000121 AC: 22AN: 181701Hom.: 0 AF XY: 0.000105 AC XY: 7AN XY: 66959
GnomAD4 exome AF: 0.0000556 AC: 61AN: 1097631Hom.: 0 Cov.: 30 AF XY: 0.0000468 AC XY: 17AN XY: 363085
GnomAD4 genome AF: 0.000267 AC: 30AN: 112485Hom.: 0 Cov.: 23 AF XY: 0.000433 AC XY: 15AN XY: 34631
ClinVar
Submissions by phenotype
not specified Uncertain:1Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Apr 02, 2014 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Uncertain significance, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Aug 14, 2016 | Variant classified as Uncertain Significance - Favor Benign. The c.-10C>T varian t in LAMP2 has not been previously reported in individuals with cardiomyopathy, but has been identified in 3/46625 European chromosomes by the Exome Aggregation Consortium (ExAC, http://exac.broadinstitute.org; dbSNP rs201209341), including 1 hemizygous individual. This variant is located in the 5' UTR. The c.-10 posit ion is poorly conserved in mammals and evolutionarily distant species and 11 mam mals carry a thymine (T) at this position, raising the possibility that this cha nge may be tolerated. In summary, while the clinical significance of this varian t is uncertain, these data suggest that it is more likely to be benign. - |
Cardiomyopathy Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CHEO Genetics Diagnostic Laboratory, Children's Hospital of Eastern Ontario | Sep 16, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at