rs746330494
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP6BS2
The NM_002294.3(LAMP2):c.865-8delT variant causes a splice region, 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, 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LAMP2 | NM_002294.3 | c.865-8delT | splice_region_variant, intron_variant | Intron 6 of 8 | ENST00000200639.9 | NP_002285.1 | ||
LAMP2 | NM_001122606.1 | c.865-8delT | splice_region_variant, intron_variant | Intron 6 of 8 | NP_001116078.1 | |||
LAMP2 | NM_013995.2 | c.865-8delT | splice_region_variant, intron_variant | Intron 6 of 8 | NP_054701.1 |
Ensembl
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
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not provided Benign:2
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Danon disease Benign:1
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LAMP2-related disorder Benign:1
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