rs377303143
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Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The ENST00000371335.4(LAMP2):c.*13C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000447 in 1,207,309 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 23 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.000045 ( 0 hom., 1 hem., cov: 23)
Exomes 𝑓: 0.000045 ( 0 hom. 22 hem. )
Consequence
LAMP2
ENST00000371335.4 3_prime_UTR
ENST00000371335.4 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.257
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 Benign. Variant got -16 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.72).
BP6
Variant X-120439141-G-A is Benign according to our data. Variant chrX-120439141-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 179017.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS2
High Hemizygotes in GnomAdExome4 at 22 XL gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LAMP2 | NM_002294.3 | c.1093+2589C>T | intron_variant | ENST00000200639.9 | |||
LAMP2 | NM_013995.2 | c.*13C>T | 3_prime_UTR_variant | 9/9 | |||
LAMP2 | NM_001122606.1 | c.1093+2589C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LAMP2 | ENST00000200639.9 | c.1093+2589C>T | intron_variant | 1 | NM_002294.3 | P3 |
Frequencies
GnomAD3 genomes AF: 0.0000448 AC: 5AN: 111721Hom.: 0 Cov.: 23 AF XY: 0.0000295 AC XY: 1AN XY: 33925
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GnomAD3 exomes AF: 0.0000382 AC: 7AN: 183341Hom.: 0 AF XY: 0.0000737 AC XY: 5AN XY: 67831
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GnomAD4 exome AF: 0.0000447 AC: 49AN: 1095537Hom.: 0 Cov.: 29 AF XY: 0.0000609 AC XY: 22AN XY: 361067
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GnomAD4 genome AF: 0.0000447 AC: 5AN: 111772Hom.: 0 Cov.: 23 AF XY: 0.0000294 AC XY: 1AN XY: 33986
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 15, 2017 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Likely benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Nov 21, 2013 | *13C>T in the 3' UTR of LAMP2: This variant is not expected to have clinical sig nificance because it is not located within the splice consensus sequence. It ha s been identified in 1/6728 European American chromosomes by the NHLBI Exome Seq uencing Project (http://evs.gs.washington.edu/EVS/; dbSNP rs377303143). *13C>T in the 3' UTR of LAMP2 (rs377303143, allele frequency = 1/6728) ** - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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