chr1-147654322-G-A
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_016361.5(ACP6):c.652C>T(p.Arg218Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0149 in 1,613,876 control chromosomes in the GnomAD database, including 225 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.010 ( 14 hom., cov: 32)
Exomes 𝑓: 0.015 ( 211 hom. )
Consequence
ACP6
NM_016361.5 missense
NM_016361.5 missense
Scores
1
6
9
Clinical Significance
Conservation
PhyloP100: 2.39
Genes affected
ACP6 (HGNC:29609): (acid phosphatase 6, lysophosphatidic) This gene encodes a member of the histidine acid phosphatase protein family. The encoded protein hydrolyzes lysophosphatidic acid, which is involved in G protein-coupled receptor signaling, lipid raft modulation, and in balancing lipid composition within the cell. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.004639417).
BP6
Variant 1-147654322-G-A is Benign according to our data. Variant chr1-147654322-G-A is described in ClinVar as [Benign]. Clinvar id is 218733.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS1
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0105 (1593/152210) while in subpopulation NFE AF= 0.0172 (1171/68010). AF 95% confidence interval is 0.0164. There are 14 homozygotes in gnomad4. There are 739 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 14 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ACP6 | NM_016361.5 | c.652C>T | p.Arg218Trp | missense_variant | 6/10 | ENST00000583509.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ACP6 | ENST00000583509.7 | c.652C>T | p.Arg218Trp | missense_variant | 6/10 | 1 | NM_016361.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0105 AC: 1593AN: 152092Hom.: 14 Cov.: 32
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GnomAD3 exomes AF: 0.0106 AC: 2671AN: 251214Hom.: 24 AF XY: 0.0114 AC XY: 1549AN XY: 135768
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GnomAD4 exome AF: 0.0153 AC: 22421AN: 1461666Hom.: 211 Cov.: 30 AF XY: 0.0153 AC XY: 11145AN XY: 727170
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GnomAD4 genome AF: 0.0105 AC: 1593AN: 152210Hom.: 14 Cov.: 32 AF XY: 0.00993 AC XY: 739AN XY: 74428
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Genomic Diagnostic Laboratory, Division of Genomic Diagnostics, Children's Hospital of Philadelphia | Mar 06, 2015 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Benign
T;.;.
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;D;D
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationAssessor
Pathogenic
M;M;.
MutationTaster
Benign
N;N
PrimateAI
Benign
T
REVEL
Benign
Sift4G
Uncertain
D;D;D
Polyphen
D;D;.
Vest4
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