chrX-40581031-G-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_005765.3(ATP6AP2):c.-35G>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00196 in 1,162,744 control chromosomes in the GnomAD database, including 27 homozygotes. There are 622 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0099 ( 18 hom., 325 hem., cov: 24)
Exomes 𝑓: 0.0011 ( 9 hom. 297 hem. )
Consequence
ATP6AP2
NM_005765.3 5_prime_UTR
NM_005765.3 5_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.00600
Genes affected
ATP6AP2 (HGNC:18305): (ATPase H+ transporting accessory protein 2) This gene encodes a protein that is associated with adenosine triphosphatases (ATPases). Proton-translocating ATPases have fundamental roles in energy conservation, secondary active transport, acidification of intracellular compartments, and cellular pH homeostasis. There are three classes of ATPases- F, P, and V. The vacuolar (V-type) ATPases have a transmembrane proton-conducting sector and an extramembrane catalytic sector. The encoded protein has been found associated with the transmembrane sector of the V-type ATPases. [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=-0.49).
BP6
?
Variant X-40581031-G-C is Benign according to our data. Variant chrX-40581031-G-C is described in ClinVar as [Benign]. Clinvar id is 136464.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00994 (1126/113284) while in subpopulation AFR AF= 0.0342 (1072/31308). AF 95% confidence interval is 0.0325. There are 18 homozygotes in gnomad4. There are 325 alleles in male gnomad4 subpopulation. Median coverage is 24. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 18 XL gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ATP6AP2 | NM_005765.3 | c.-35G>C | 5_prime_UTR_variant | 1/9 | ENST00000636580.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATP6AP2 | ENST00000636580.2 | c.-35G>C | 5_prime_UTR_variant | 1/9 | 1 | NM_005765.3 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.00994 AC: 1125AN: 113235Hom.: 18 Cov.: 24 AF XY: 0.00915 AC XY: 324AN XY: 35401
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GnomAD3 exomes AF: 0.00237 AC: 245AN: 103268Hom.: 1 AF XY: 0.00149 AC XY: 55AN XY: 36924
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GnomAD4 exome AF: 0.00110 AC: 1157AN: 1049460Hom.: 9 Cov.: 30 AF XY: 0.000867 AC XY: 297AN XY: 342370
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GnomAD4 genome ? AF: 0.00994 AC: 1126AN: 113284Hom.: 18 Cov.: 24 AF XY: 0.00917 AC XY: 325AN XY: 35460
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Feb 28, 2013 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at