rs397516737
Positions:
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_002294.3(LAMP2):c.184-7C>G variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 20)
Consequence
LAMP2
NM_002294.3 splice_region, splice_polypyrimidine_tract, intron
NM_002294.3 splice_region, splice_polypyrimidine_tract, intron
Scores
2
Splicing: ADA: 0.0002611
2
Clinical Significance
Conservation
PhyloP100: 0.264
Genes affected
LAMP2 (HGNC:6501): (lysosomal associated membrane protein 2) The protein encoded by this gene is a member of a family of membrane glycoproteins. This glycoprotein provides selectins with carbohydrate ligands. It may play a role in tumor cell metastasis. It may also function in the protection, maintenance, and adhesion of the lysosome. Alternative splicing of this gene results in multiple transcript variants encoding distinct proteins. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.8).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LAMP2 | NM_002294.3 | c.184-7C>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000200639.9 | |||
LAMP2 | NM_001122606.1 | c.184-7C>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ||||
LAMP2 | NM_013995.2 | c.184-7C>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LAMP2 | ENST00000200639.9 | c.184-7C>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_002294.3 | P3 | |||
LAMP2 | ENST00000371335.4 | c.184-7C>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | A1 | ||||
LAMP2 | ENST00000434600.6 | c.184-7C>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | A1 | ||||
LAMP2 | ENST00000706600.1 | c.184-7C>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant |
Frequencies
GnomAD3 genomes ? Cov.: 20
GnomAD3 genomes
?
Cov.:
20
GnomAD4 exome Cov.: 27
GnomAD4 exome
Cov.:
27
GnomAD4 genome ? Cov.: 20
GnomAD4 genome
?
Cov.:
20
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Jun 25, 2010 | Variant classified as Uncertain Significance - Favor Pathogenic. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Name
Calibrated prediction
Score
Prediction
dbscSNV1_ADA
Benign
dbscSNV1_RF
Benign
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at