chr11-47246999-T-G
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001610.4(ACP2):c.297+642A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.397 in 152,002 control chromosomes in the GnomAD database, including 13,211 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 0.40 ( 13211 hom., cov: 32)
Consequence
ACP2
NM_001610.4 intron
NM_001610.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.245
Publications
12 publications found
Genes affected
ACP2 (HGNC:123): (acid phosphatase 2, lysosomal) The protein encoded by this gene belongs to the histidine acid phosphatase family, which hydrolyze orthophosphoric monoesters to alcohol and phosphate. This protein is localized to the lysosomal membrane, and is chemically and genetically distinct from the red cell acid phosphatase. Mice lacking this gene showed multiple defects, including bone structure alterations, lysosomal storage defects, and an increased tendency towards seizures. An enzymatically-inactive allele of this gene in mice showed severe growth retardation, hair-follicle abnormalities, and an ataxia-like phenotype. Alternatively spliced transcript variants have been found for this gene. A C-terminally extended isoform is also predicted to be produced by the use of an alternative in-frame translation termination codon via a stop codon readthrough mechanism. [provided by RefSeq, Oct 2017]
ACP2 Gene-Disease associations (from GenCC):
- lysosomal acid phosphatase deficiencyInheritance: Unknown Classification: NO_KNOWN Submitted by: Labcorp Genetics (formerly Invitae)
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.727 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.397 AC: 60261AN: 151884Hom.: 13201 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
60261
AN:
151884
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.397 AC: 60302AN: 152002Hom.: 13211 Cov.: 32 AF XY: 0.407 AC XY: 30203AN XY: 74288 show subpopulations
GnomAD4 genome
AF:
AC:
60302
AN:
152002
Hom.:
Cov.:
32
AF XY:
AC XY:
30203
AN XY:
74288
show subpopulations
African (AFR)
AF:
AC:
22203
AN:
41448
American (AMR)
AF:
AC:
5486
AN:
15268
Ashkenazi Jewish (ASJ)
AF:
AC:
776
AN:
3464
East Asian (EAS)
AF:
AC:
3862
AN:
5174
South Asian (SAS)
AF:
AC:
2244
AN:
4814
European-Finnish (FIN)
AF:
AC:
4517
AN:
10552
Middle Eastern (MID)
AF:
AC:
78
AN:
294
European-Non Finnish (NFE)
AF:
AC:
20310
AN:
67966
Other (OTH)
AF:
AC:
705
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.504
Heterozygous variant carriers
0
1764
3529
5293
7058
8822
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
1904
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
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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