rs10504978
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_018407.6(LAPTM4B):c.211+132T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0243 in 644,604 control chromosomes in the GnomAD database, including 1,133 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 0.061 ( 826 hom., cov: 31)
Exomes 𝑓: 0.013 ( 307 hom. )
Consequence
LAPTM4B
NM_018407.6 intron
NM_018407.6 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.140
Genes affected
LAPTM4B (HGNC:13646): (lysosomal protein transmembrane 4 beta) Enables ceramide binding activity; enzyme binding activity; and phosphatidylinositol bisphosphate binding activity. Involved in several processes, including negative regulation of macromolecule metabolic process; regulation of lysosomal membrane permeability; and regulation of lysosome organization. Located in several cellular components, including endosome; lysosomal membrane; and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]
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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=-0.91).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.19 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LAPTM4B | NM_018407.6 | c.211+132T>C | intron_variant | ENST00000521545.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LAPTM4B | ENST00000521545.7 | c.211+132T>C | intron_variant | 1 | NM_018407.6 | P1 | |||
LAPTM4B | ENST00000445593.6 | c.484+132T>C | intron_variant | 1 | |||||
LAPTM4B | ENST00000619747.1 | c.484+132T>C | intron_variant | 1 | |||||
LAPTM4B | ENST00000517924.5 | c.211+132T>C | intron_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0612 AC: 9307AN: 152110Hom.: 826 Cov.: 31
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GnomAD4 exome AF: 0.0129 AC: 6368AN: 492376Hom.: 307 AF XY: 0.0121 AC XY: 3199AN XY: 263514
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GnomAD4 genome ? AF: 0.0613 AC: 9324AN: 152228Hom.: 826 Cov.: 31 AF XY: 0.0597 AC XY: 4447AN XY: 74438
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at