chrX-154428710-G-T
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_001183.6(ATP6AP1):c.18G>T(p.Ala6Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000193 in 1,035,685 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: not found (cov: 25)
Exomes 𝑓: 0.0000019 ( 0 hom. 0 hem. )
Consequence
ATP6AP1
NM_001183.6 synonymous
NM_001183.6 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0280
Publications
0 publications found
Genes affected
ATP6AP1 (HGNC:868): (ATPase H+ transporting accessory protein 1) This gene encodes a component of a multisubunit enzyme that mediates acidification of eukaryotic intracellular organelles. Vacuolar ATPase (V-ATPase) is comprised of a cytosolic V1 (site of the ATP catalytic site) and a transmembrane V0 domain. V-ATPase dependent organelle acidification is necessary for such intracellular processes as protein sorting, zymogen activation, and receptor-mediated endocytosis. The encoded protein of this gene may assist in the V-ATPase-mediated acidification of neuroendocrine secretory granules. This protein may also play a role in early development. [provided by RefSeq, Aug 2013]
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ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.36).
BP6
Variant X-154428710-G-T is Benign according to our data. Variant chrX-154428710-G-T is described in ClinVar as [Likely_benign]. Clinvar id is 1548391.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.028 with no splicing effect.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
25
GnomAD4 exome AF: 0.00000193 AC: 2AN: 1035685Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 336471 show subpopulations
GnomAD4 exome
AF:
AC:
2
AN:
1035685
Hom.:
Cov.:
30
AF XY:
AC XY:
0
AN XY:
336471
show subpopulations
African (AFR)
AF:
AC:
0
AN:
22667
American (AMR)
AF:
AC:
0
AN:
27167
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
18212
East Asian (EAS)
AF:
AC:
0
AN:
25371
South Asian (SAS)
AF:
AC:
0
AN:
49275
European-Finnish (FIN)
AF:
AC:
0
AN:
30018
Middle Eastern (MID)
AF:
AC:
0
AN:
3987
European-Non Finnish (NFE)
AF:
AC:
2
AN:
815144
Other (OTH)
AF:
AC:
0
AN:
43844
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.450
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
GnomAD4 genome
Cov.:
25
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Jul 05, 2022
Labcorp Genetics (formerly Invitae), Labcorp
Significance:Likely benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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