chrX-40580909-T-C
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_ModerateBP6_ModerateBS1BS2
The ENST00000636409.1(ATP6AP2):c.-157T>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 0.00288 in 634,424 control chromosomes in the GnomAD database, including 24 homozygotes. There are 465 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.010 ( 14 hom., 306 hem., cov: 25)
Exomes 𝑓: 0.0013 ( 10 hom. 159 hem. )
Consequence
ATP6AP2
ENST00000636409.1 5_prime_UTR
ENST00000636409.1 5_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.00500
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 -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.39).
BP6
?
Variant X-40580909-T-C is Benign according to our data. Variant chrX-40580909-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 673879.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0101 (1136/112846) while in subpopulation AFR AF= 0.0348 (1083/31117). AF 95% confidence interval is 0.0331. There are 14 homozygotes in gnomad4. There are 306 alleles in male gnomad4 subpopulation. Median coverage is 25. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 14 XL gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATP6AP2 | ENST00000636409.1 | c.-157T>C | 5_prime_UTR_variant | 1/8 | 2 | ||||
ATP6AP2 | ENST00000436783.6 | c.-111+1162T>C | intron_variant | 5 | |||||
ATP6AP2 | ENST00000487051.2 | n.10T>C | non_coding_transcript_exon_variant | 1/3 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0101 AC: 1137AN: 112797Hom.: 14 Cov.: 25 AF XY: 0.00875 AC XY: 306AN XY: 34983
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GnomAD4 exome AF: 0.00132 AC: 691AN: 521578Hom.: 10 Cov.: 8 AF XY: 0.000986 AC XY: 159AN XY: 161302
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GnomAD4 genome ? AF: 0.0101 AC: 1136AN: 112846Hom.: 14 Cov.: 25 AF XY: 0.00873 AC XY: 306AN XY: 35042
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 19, 2018 | 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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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