rs746330494
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP6BS2
The NM_002294.3(LAMP2):c.865-8del variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000262 in 1,069,203 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 9 hemizygotes in GnomAD. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_002294.3 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LAMP2 | NM_002294.3 | c.865-8del | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000200639.9 | |||
LAMP2 | NM_001122606.1 | c.865-8del | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ||||
LAMP2 | NM_013995.2 | c.865-8del | 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.865-8del | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_002294.3 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.00 AC: 1AN: 111824Hom.: 0 Cov.: 22 AF XY: 0.0000294 AC XY: 1AN XY: 34054 FAILED QC
GnomAD3 exomes AF: 0.0000438 AC: 8AN: 182769Hom.: 0 AF XY: 0.0000297 AC XY: 2AN XY: 67343
GnomAD4 exome AF: 0.0000262 AC: 28AN: 1069203Hom.: 0 Cov.: 27 AF XY: 0.0000267 AC XY: 9AN XY: 336501
GnomAD4 genome ? Data not reliable, filtered out with message: AS_VQSR AF: 0.00000894 AC: 1AN: 111824Hom.: 0 Cov.: 22 AF XY: 0.0000294 AC XY: 1AN XY: 34054
ClinVar
Submissions by phenotype
not specified Uncertain:1Benign:1
Benign, no assertion criteria provided | clinical testing | Clinical Genetics, Academic Medical Center | - | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Sep 16, 2023 | - - |
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jan 30, 2020 | - - |
Likely benign, no assertion criteria provided | clinical testing | Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen | - | - - |
Danon disease Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 10, 2024 | - - |
LAMP2-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Aug 13, 2020 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at