chr6-31544943-G-C
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_130463.4(ATP6V1G2):c.*465C>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.36 in 360,030 control chromosomes in the GnomAD database, including 24,205 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 0.38 ( 11611 hom., cov: 32)
Exomes 𝑓: 0.34 ( 12594 hom. )
Consequence
ATP6V1G2
NM_130463.4 3_prime_UTR
NM_130463.4 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.876
Genes affected
ATP6V1G2 (HGNC:862): (ATPase H+ transporting V1 subunit G2) This gene encodes a component of vacuolar ATPase (V-ATPase), a multisubunit enzyme that mediates acidification of intracellular compartments of eukaryotic cells. V-ATPase dependent 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 and three B subunits, two G subunits plus the C, D, E, F, and H subunits. The V1 domain contains the ATP catalytic site. The V0 domain consists of five different subunits: a, c, c', c'', and d. Additional isoforms of many of the V1 and V0 subunit proteins are encoded by multiple genes or alternatively spliced transcript variants. This encoded protein is one of three V1 domain G subunit proteins. This gene had previous gene symbols of ATP6G and ATP6G2. Alternatively spliced transcript variants encoding different isoforms have been described. Read-through transcription also exists between this gene and the downstream DEAD (Asp-Glu-Ala-Asp) box polypeptide 39B (DDX39B) gene. [provided by RefSeq, Feb 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=-0.84).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.496 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ATP6V1G2 | NM_130463.4 | c.*465C>G | 3_prime_UTR_variant | 3/3 | ENST00000303892.10 | ||
ATP6V1G2-DDX39B | NR_037853.1 | n.472+1166C>G | intron_variant, non_coding_transcript_variant | ||||
ATP6V1G2 | NM_001204078.2 | c.*465C>G | 3_prime_UTR_variant | 3/3 | |||
ATP6V1G2 | NM_138282.3 | c.*465C>G | 3_prime_UTR_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATP6V1G2 | ENST00000303892.10 | c.*465C>G | 3_prime_UTR_variant | 3/3 | 1 | NM_130463.4 | P1 | ||
ATP6V1G2 | ENST00000376151.4 | c.*465C>G | 3_prime_UTR_variant | 3/3 | 1 |
Frequencies
GnomAD3 genomes AF: 0.383 AC: 58188AN: 151860Hom.: 11599 Cov.: 32
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GnomAD4 exome AF: 0.343 AC: 71447AN: 208052Hom.: 12594 Cov.: 0 AF XY: 0.337 AC XY: 38843AN XY: 115186
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GnomAD4 genome AF: 0.383 AC: 58239AN: 151978Hom.: 11611 Cov.: 32 AF XY: 0.379 AC XY: 28158AN XY: 74282
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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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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at