rs2286241
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The NM_004047.5(ATP6V0B):āc.57G>Cā(p.Ala19=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0563 in 1,407,126 control chromosomes in the GnomAD database, including 2,569 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: š 0.058 ( 283 hom., cov: 33)
Exomes š: 0.056 ( 2286 hom. )
Consequence
ATP6V0B
NM_004047.5 synonymous
NM_004047.5 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.515
Genes affected
ATP6V0B (HGNC:861): (ATPase H+ transporting V0 subunit b) This gene encodes a portion of the V0 domain of vacuolar ATPase (V-ATPase), a multisubunit enzyme that mediates acidification of eukaryotic intracellular organelles. Activity of this enzyme is necessary for such varied processes as protein sorting, zymogen activation, receptor-mediated endocytosis, and synaptic vesicle proton gradient generation. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jun 2014]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.65).
BP7
?
Synonymous conserved (PhyloP=0.515 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.158 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ATP6V0B | NM_004047.5 | c.57G>C | p.Ala19= | synonymous_variant | 1/8 | ENST00000472174.7 | |
ATP6V0B | NM_001294333.2 | c.57G>C | p.Ala19= | synonymous_variant | 1/7 | ||
ATP6V0B | NM_001039457.3 | c.-36G>C | 5_prime_UTR_variant | 1/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATP6V0B | ENST00000472174.7 | c.57G>C | p.Ala19= | synonymous_variant | 1/8 | 1 | NM_004047.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0584 AC: 8886AN: 152180Hom.: 282 Cov.: 33
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GnomAD3 exomes AF: 0.0580 AC: 1524AN: 26288Hom.: 69 AF XY: 0.0582 AC XY: 793AN XY: 13616
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GnomAD4 exome AF: 0.0561 AC: 70337AN: 1254828Hom.: 2286 Cov.: 31 AF XY: 0.0562 AC XY: 34288AN XY: 610496
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GnomAD4 genome ? AF: 0.0584 AC: 8900AN: 152298Hom.: 283 Cov.: 33 AF XY: 0.0593 AC XY: 4419AN XY: 74472
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ClinVar
Not reported inComputational scores
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Name
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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