chr8-20209624-T-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001693.4(ATP6V1B2):c.291+93T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0394 in 1,201,162 control chromosomes in the GnomAD database, including 1,242 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.043 ( 165 hom., cov: 32)
Exomes 𝑓: 0.039 ( 1077 hom. )
Consequence
ATP6V1B2
NM_001693.4 intron
NM_001693.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.692
Genes affected
ATP6V1B2 (HGNC:854): (ATPase H+ transporting V1 subunit B2) This gene encodes a component of vacuolar ATPase (V-ATPase), a multisubunit enzyme that mediates acidification of eukaryotic intracellular organelles. V-ATPase dependent organelle acidification is necessary for such intracellular processes as protein sorting, zymogen activation, receptor-mediated endocytosis, and synaptic vesicle proton gradient generation. V-ATPase is composed of a cytosolic V1 domain and a transmembrane V0 domain. The V1 domain consists of three A, three B, and two G subunits, as well as a C, D, E, F, and H subunit. The V1 domain contains the ATP catalytic site. The protein encoded by this gene is one of two V1 domain B subunit isoforms and is the only B isoform highly expressed in osteoclasts. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BP6
?
Variant 8-20209624-T-G is Benign according to our data. Variant chr8-20209624-T-G is described in ClinVar as [Benign]. Clinvar id is 1250071.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.064 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ATP6V1B2 | NM_001693.4 | c.291+93T>G | intron_variant | ENST00000276390.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATP6V1B2 | ENST00000276390.7 | c.291+93T>G | intron_variant | 1 | NM_001693.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0428 AC: 6503AN: 152068Hom.: 163 Cov.: 32
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GnomAD4 exome AF: 0.0390 AC: 40872AN: 1048976Hom.: 1077 AF XY: 0.0387 AC XY: 20670AN XY: 533802
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GnomAD4 genome ? AF: 0.0428 AC: 6506AN: 152186Hom.: 165 Cov.: 32 AF XY: 0.0429 AC XY: 3191AN XY: 74414
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 16, 2021 | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at