chr3-132328294-A-C

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_001099.5(ACP3):ā€‹c.148A>Cā€‹(p.Ile50Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000274 in 1,461,646 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 31)
Exomes š‘“: 0.0000027 ( 0 hom. )

Consequence

ACP3
NM_001099.5 missense

Scores

3
16

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.356
Variant links:
Genes affected
ACP3 (HGNC:125): (acid phosphatase 3) This gene encodes an enzyme that catalyzes the conversion of orthophosphoric monoester to alcohol and orthophosphate. It is synthesized under androgen regulation and is secreted by the epithelial cells of the prostate gland. An alternatively spliced transcript variant encoding a longer isoform has been found for this gene. This isoform contains a transmembrane domain and is localized in the plasma membrane-endosomal-lysosomal pathway. [provided by RefSeq, Sep 2008]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.15052229).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ACP3NM_001099.5 linkc.148A>C p.Ile50Leu missense_variant Exon 2 of 10 ENST00000336375.10 NP_001090.2 P15309-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ACP3ENST00000336375.10 linkc.148A>C p.Ile50Leu missense_variant Exon 2 of 10 1 NM_001099.5 ENSP00000337471.5 P15309-1

Frequencies

GnomAD3 genomes
Cov.:
31
GnomAD4 exome
AF:
0.00000274
AC:
4
AN:
1461646
Hom.:
0
Cov.:
30
AF XY:
0.00000138
AC XY:
1
AN XY:
727136
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000360
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
31
Alfa
AF:
0.0000282
Hom.:
0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.18
BayesDel_addAF
Benign
-0.13
T
BayesDel_noAF
Benign
-0.43
CADD
Uncertain
24
DANN
Uncertain
0.99
DEOGEN2
Benign
0.20
T;T;.;.
Eigen
Benign
0.16
Eigen_PC
Uncertain
0.27
FATHMM_MKL
Uncertain
0.79
D
LIST_S2
Benign
0.81
T;T;D;D
M_CAP
Benign
0.0095
T
MetaRNN
Benign
0.15
T;T;T;T
MetaSVM
Benign
-0.96
T
MutationAssessor
Benign
1.3
L;.;L;L
PrimateAI
Benign
0.46
T
PROVEAN
Benign
-1.2
N;N;N;N
REVEL
Benign
0.11
Sift
Benign
0.31
T;T;T;T
Sift4G
Benign
0.26
T;T;T;T
Polyphen
0.30
B;.;.;B
Vest4
0.49
MutPred
0.45
Gain of disorder (P = 0.1264);Gain of disorder (P = 0.1264);Gain of disorder (P = 0.1264);Gain of disorder (P = 0.1264);
MVP
0.076
MPC
0.26
ClinPred
0.57
D
GERP RS
5.7
Varity_R
0.44
gMVP
0.24

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs768803310; hg19: chr3-132047138; API