8-20197446-G-T
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001693.4(ATP6V1B2):c.40G>T(p.Ala14Ser) variant causes a missense change. The variant allele was found at a frequency of 0.0019 in 1,542,432 control chromosomes in the GnomAD database, including 49 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.010 ( 24 hom., cov: 33)
Exomes 𝑓: 0.00099 ( 25 hom. )
Consequence
ATP6V1B2
NM_001693.4 missense
NM_001693.4 missense
Scores
2
16
Clinical Significance
Conservation
PhyloP100: 4.24
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 -20 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.003306955).
BP6
Variant 8-20197446-G-T is Benign according to our data. Variant chr8-20197446-G-T is described in ClinVar as [Benign]. Clinvar id is 783518.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0102 (1557/152280) while in subpopulation AFR AF= 0.0355 (1477/41572). AF 95% confidence interval is 0.034. There are 24 homozygotes in gnomad4. There are 720 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
High AC in GnomAd4 at 1557 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ATP6V1B2 | NM_001693.4 | c.40G>T | p.Ala14Ser | missense_variant | 1/14 | ENST00000276390.7 | NP_001684.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0102 AC: 1554AN: 152162Hom.: 24 Cov.: 33
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GnomAD3 exomes AF: 0.00233 AC: 391AN: 167726Hom.: 9 AF XY: 0.00175 AC XY: 163AN XY: 93308
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GnomAD4 exome AF: 0.000986 AC: 1370AN: 1390152Hom.: 25 Cov.: 31 AF XY: 0.000868 AC XY: 599AN XY: 690370
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GnomAD4 genome AF: 0.0102 AC: 1557AN: 152280Hom.: 24 Cov.: 33 AF XY: 0.00967 AC XY: 720AN XY: 74460
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 31, 2019 | - - |
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
DEOGEN2
Benign
T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Benign
N
PrimateAI
Uncertain
T
PROVEAN
Benign
N
REVEL
Benign
Sift
Benign
T
Sift4G
Benign
T
Polyphen
P
Vest4
MVP
MPC
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
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