rs1301008847
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Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 1P and 6B. PP3BP6_ModerateBS2
The ENST00000371335.4(LAMP2):āc.1142T>Cā(p.Val381Ala) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000207 in 1,207,913 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 7 hemizygotes in GnomAD. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Genomes: š 0.00012 ( 0 hom., 2 hem., cov: 23)
Exomes š: 0.000011 ( 0 hom. 5 hem. )
Consequence
LAMP2
ENST00000371335.4 missense
ENST00000371335.4 missense
Scores
5
4
4
Clinical Significance
Conservation
PhyloP100: 8.95
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 -5 ACMG points.
PP3
?
MetaRNN computational evidence supports a deleterious effect, 0.795
BP6
?
Variant X-120439245-A-G is Benign according to our data. Variant chrX-120439245-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 532013.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High Hemizygotes in GnomAd4 at 2 XL gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LAMP2 | NM_002294.3 | c.1093+2485T>C | intron_variant | ENST00000200639.9 | |||
LAMP2 | NM_013995.2 | c.1142T>C | p.Val381Ala | missense_variant | 9/9 | ||
LAMP2 | NM_001122606.1 | c.1093+2485T>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LAMP2 | ENST00000200639.9 | c.1093+2485T>C | intron_variant | 1 | NM_002294.3 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.000116 AC: 13AN: 111905Hom.: 0 Cov.: 23 AF XY: 0.0000587 AC XY: 2AN XY: 34097
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GnomAD3 exomes AF: 0.0000164 AC: 3AN: 183327Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 67827
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GnomAD4 exome AF: 0.0000109 AC: 12AN: 1096008Hom.: 0 Cov.: 28 AF XY: 0.0000138 AC XY: 5AN XY: 361462
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GnomAD4 genome ? AF: 0.000116 AC: 13AN: 111905Hom.: 0 Cov.: 23 AF XY: 0.0000587 AC XY: 2AN XY: 34097
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Danon disease Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Mar 09, 2022 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Benign
T
M_CAP
Pathogenic
D
MetaRNN
Pathogenic
D
MetaSVM
Uncertain
T
MutationTaster
Benign
D;D;D;D;D
PROVEAN
Uncertain
D
REVEL
Uncertain
Sift
Pathogenic
D
Sift4G
Pathogenic
D
Polyphen
D
Vest4
MVP
ClinPred
D
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at