rs10987251
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_033446.3(MVB12B):c.204+85G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.312 in 1,481,558 control chromosomes in the GnomAD database, including 72,478 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 0.30 ( 6912 hom., cov: 32)
Exomes 𝑓: 0.31 ( 65566 hom. )
Consequence
MVB12B
NM_033446.3 intron
NM_033446.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.270
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 Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.312 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MVB12B | NM_033446.3 | c.204+85G>A | intron_variant | ENST00000361171.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MVB12B | ENST00000361171.8 | c.204+85G>A | intron_variant | 2 | NM_033446.3 | P1 | |||
MVB12B | ENST00000489637.3 | c.204+85G>A | intron_variant | 1 | |||||
MVB12B | ENST00000402437.2 | c.159+85G>A | intron_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.300 AC: 45572AN: 151968Hom.: 6912 Cov.: 32
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GnomAD4 exome AF: 0.313 AC: 416333AN: 1329472Hom.: 65566 AF XY: 0.312 AC XY: 205251AN XY: 658878
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GnomAD4 genome ? AF: 0.300 AC: 45588AN: 152086Hom.: 6912 Cov.: 32 AF XY: 0.302 AC XY: 22485AN XY: 74338
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ClinVar
Not reported inComputational scores
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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