rs531599
Positions:
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_033446.3(MVB12B):c.82-1398C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00225 in 152,242 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.0022 ( 0 hom., cov: 33)
Consequence
MVB12B
NM_033446.3 intron
NM_033446.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.54
Genes affected
MVB12B (HGNC:23368): (multivesicular body subunit 12B) The protein encoded by this gene is a component of the ESCRT-I complex, a heterotetramer, which mediates the sorting of ubiquitinated cargo protein from the plasma membrane to the endosomal vesicle. ESCRT-I complex plays an essential role in HIV budding and endosomal protein sorting. Depletion and overexpression of this and related protein (MVB12A) inhibit HIV-1 infectivity and induce unusual viral assembly defects, indicating a role for MVB12 subunits in regulating ESCRT-mediated virus budding. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2011]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MVB12B | NM_033446.3 | c.82-1398C>A | intron_variant | ENST00000361171.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MVB12B | ENST00000361171.8 | c.82-1398C>A | intron_variant | 2 | NM_033446.3 | P1 | |||
MVB12B | ENST00000489637.3 | c.82-1398C>A | intron_variant | 1 | |||||
MVB12B | ENST00000402437.2 | c.37-1398C>A | intron_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.00225 AC: 343AN: 152122Hom.: 0 Cov.: 33
GnomAD3 genomes
?
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152122
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33
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.00225 AC: 342AN: 152242Hom.: 0 Cov.: 33 AF XY: 0.00212 AC XY: 158AN XY: 74434
GnomAD4 genome
?
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152242
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158
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74434
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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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