NM_002294.3:c.697C>T
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_002294.3(LAMP2):c.697C>T(p.Leu233Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000911 in 1,097,618 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. L233L) has been classified as Likely benign.
Frequency
Genomes: not found (cov: 23)
Exomes 𝑓: 9.1e-7 ( 0 hom. 0 hem. )
Consequence
LAMP2
NM_002294.3 synonymous
NM_002294.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 2.04
Publications
0 publications found
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]
LAMP2 Gene-Disease associations (from GenCC):
- Danon diseaseInheritance: XL Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: ClinGen, G2P, Labcorp Genetics (formerly Invitae), Genomics England PanelApp, Orphanet
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.41).
BP6
Variant X-120447885-G-A is Benign according to our data. Variant chrX-120447885-G-A is described in ClinVar as Likely_benign. ClinVar VariationId is 2128806.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=2.04 with no splicing effect.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| LAMP2 | NM_002294.3 | c.697C>T | p.Leu233Leu | synonymous_variant | Exon 5 of 9 | ENST00000200639.9 | NP_002285.1 | |
| LAMP2 | NM_001122606.1 | c.697C>T | p.Leu233Leu | synonymous_variant | Exon 5 of 9 | NP_001116078.1 | ||
| LAMP2 | NM_013995.2 | c.697C>T | p.Leu233Leu | synonymous_variant | Exon 5 of 9 | NP_054701.1 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| LAMP2 | ENST00000200639.9 | c.697C>T | p.Leu233Leu | synonymous_variant | Exon 5 of 9 | 1 | NM_002294.3 | ENSP00000200639.4 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
23
GnomAD4 exome AF: 9.11e-7 AC: 1AN: 1097618Hom.: 0 Cov.: 29 AF XY: 0.00 AC XY: 0AN XY: 362990 show subpopulations
GnomAD4 exome
AF:
AC:
1
AN:
1097618
Hom.:
Cov.:
29
AF XY:
AC XY:
0
AN XY:
362990
show subpopulations
African (AFR)
AF:
AC:
0
AN:
26391
American (AMR)
AF:
AC:
0
AN:
35205
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
19381
East Asian (EAS)
AF:
AC:
0
AN:
30203
South Asian (SAS)
AF:
AC:
0
AN:
54130
European-Finnish (FIN)
AF:
AC:
0
AN:
40531
Middle Eastern (MID)
AF:
AC:
0
AN:
4135
European-Non Finnish (NFE)
AF:
AC:
1
AN:
841565
Other (OTH)
AF:
AC:
0
AN:
46077
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.475
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
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>80
Age
GnomAD4 genome
GnomAD4 genome
Cov.:
23
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Danon disease Benign:1
Apr 21, 2022
Labcorp Genetics (formerly Invitae), Labcorp
Significance:Likely benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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