rs12493050
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_014398.4(LAMP3):c.888+5090C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.747 in 151,860 control chromosomes in the GnomAD database, including 42,736 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.75 ( 42736 hom., cov: 29)
Consequence
LAMP3
NM_014398.4 intron
NM_014398.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.341
Genes affected
LAMP3 (HGNC:14582): (lysosomal associated membrane protein 3) Dendritic cells (DCs) are the most potent antigen-presenting cells. Immature DCs efficiently capture antigens and differentiate into interdigitating dendritic cells (IDCs) in lymphoid tissues that induce primary T-cell responses (summary by de Saint-Vis et al., 1998 [PubMed 9768752]).[supplied by OMIM, Dec 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.79 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LAMP3 | NM_014398.4 | c.888+5090C>T | intron_variant | ENST00000265598.8 | |||
LAMP3 | XM_005247360.6 | c.888+5090C>T | intron_variant | ||||
LAMP3 | XM_011512688.3 | c.888+5090C>T | intron_variant | ||||
LAMP3 | XM_047447967.1 | c.888+5090C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LAMP3 | ENST00000265598.8 | c.888+5090C>T | intron_variant | 1 | NM_014398.4 | P2 | |||
LAMP3 | ENST00000466939.1 | c.816+5090C>T | intron_variant | 2 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.747 AC: 113392AN: 151740Hom.: 42714 Cov.: 29
GnomAD3 genomes
?
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113392
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151740
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29
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.747 AC: 113475AN: 151860Hom.: 42736 Cov.: 29 AF XY: 0.749 AC XY: 55606AN XY: 74226
GnomAD4 genome
?
AF:
AC:
113475
AN:
151860
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Cov.:
29
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55606
AN XY:
74226
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Asia WGS
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2666
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
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