rs764278197
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1
The ENST00000445593.6(LAPTM4B):c.207_222dup(p.Ser75AlafsTer71) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.139 in 1,449,128 control chromosomes in the GnomAD database, including 14,898 homozygotes. Variant has been reported in ClinVar as Benign (★). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: 𝑓 0.12 ( 1178 hom., cov: 31)
Exomes 𝑓: 0.14 ( 13720 hom. )
Consequence
LAPTM4B
ENST00000445593.6 frameshift
ENST00000445593.6 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.0660
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 -10 ACMG points.
BP6
?
Variant 8-97775937-C-CGGCGGGCTCCAGGCGA is Benign according to our data. Variant chr8-97775937-C-CGGCGGGCTCCAGGCGA is described in ClinVar as [Benign]. Clinvar id is 403028.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.153 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LAPTM4B | NM_018407.6 | c.-67_-52dup | 5_prime_UTR_variant | 1/7 | ENST00000521545.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LAPTM4B | ENST00000445593.6 | c.207_222dup | p.Ser75AlafsTer71 | frameshift_variant | 1/7 | 1 | |||
LAPTM4B | ENST00000619747.1 | c.207_222dup | p.Ser75AlafsTer71 | frameshift_variant | 1/7 | 1 | |||
LAPTM4B | ENST00000521545.7 | c.-67_-52dup | 5_prime_UTR_variant | 1/7 | 1 | NM_018407.6 | P1 | ||
LAPTM4B | ENST00000517924.5 | c.-67_-52dup | 5_prime_UTR_variant | 1/5 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.116 AC: 17567AN: 151766Hom.: 1178 Cov.: 31
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GnomAD3 exomes AF: 0.0649 AC: 4110AN: 63330Hom.: 267 AF XY: 0.0652 AC XY: 2382AN XY: 36534
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GnomAD4 exome AF: 0.142 AC: 184513AN: 1297252Hom.: 13720 Cov.: 35 AF XY: 0.142 AC XY: 90428AN XY: 637568
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Mar 29, 2016 | Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Not present in FAST (frequency). ExAC: 23.9% (9166/38406) total chromosomes - |
Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at