rs7576247
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1
The NM_004300.4(ACP1):c.317A>G(p.Gln106Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.33 in 1,598,632 control chromosomes in the GnomAD database, including 89,383 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).
Frequency
Genomes: 𝑓 0.30 ( 6943 hom., cov: 33)
Exomes 𝑓: 0.33 ( 82440 hom. )
Consequence
ACP1
NM_004300.4 missense
NM_004300.4 missense
Scores
2
15
Clinical Significance
Conservation
PhyloP100: 2.79
Genes affected
ACP1 (HGNC:122): (acid phosphatase 1) The product of this gene belongs to the phosphotyrosine protein phosphatase family of proteins. It functions as an acid phosphatase and a protein tyrosine phosphatase by hydrolyzing protein tyrosine phosphate to protein tyrosine and orthophosphate. This enzyme also hydrolyzes orthophosphoric monoesters to alcohol and orthophosphate. This gene is genetically polymorphic, and three common alleles segregating at the corresponding locus give rise to six phenotypes. Each allele appears to encode at least two electrophoretically different isozymes, Bf and Bs, which are produced in allele-specific ratios. Multiple alternatively spliced transcript variants encoding distinct isoforms have been identified for this gene. [provided by RefSeq, Aug 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.003926754).
BP6
?
Variant 2-277003-A-G is Benign according to our data. Variant chr2-277003-A-G is described in ClinVar as [Benign]. Clinvar id is 13685.Status of the report is no_assertion_criteria_provided, 0 stars.
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.343 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ACP1 | NM_004300.4 | c.317A>G | p.Gln106Arg | missense_variant | 5/6 | ENST00000272065.10 | |
ACP1 | NM_007099.4 | c.317A>G | p.Gln106Arg | missense_variant | 5/6 | ||
ACP1 | NR_024080.2 | n.364A>G | non_coding_transcript_exon_variant | 6/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ACP1 | ENST00000272065.10 | c.317A>G | p.Gln106Arg | missense_variant | 5/6 | 1 | NM_004300.4 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.295 AC: 44899AN: 152026Hom.: 6950 Cov.: 33
GnomAD3 genomes
?
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GnomAD3 exomes AF: 0.310 AC: 76287AN: 245720Hom.: 12201 AF XY: 0.314 AC XY: 41674AN XY: 132876
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GnomAD4 exome AF: 0.333 AC: 482181AN: 1446486Hom.: 82440 Cov.: 30 AF XY: 0.333 AC XY: 239998AN XY: 719940
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GnomAD4 genome ? AF: 0.295 AC: 44897AN: 152146Hom.: 6943 Cov.: 33 AF XY: 0.296 AC XY: 22035AN XY: 74366
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1287
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1296
ESP6500AA
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983
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2959
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38242
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939
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
ACID PHOSPHATASE 1, SOLUBLE, A/B POLYMORPHISM OF Benign:1
Benign, no assertion criteria provided | literature only | OMIM | Aug 12, 2020 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Uncertain
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T;T
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationAssessor
Benign
N;N
MutationTaster
Benign
P;P
PrimateAI
Benign
T
PROVEAN
Benign
N;N
REVEL
Benign
Sift
Benign
T;T
Sift4G
Benign
T;T
Polyphen
B;B
Vest4
MPC
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at