chr1-147659496-C-T
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Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PP5_ModerateBP4BS2_Supporting
The NM_016361.5(ACP6):c.379G>A(p.Val127Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000899 in 1,614,212 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★).
Frequency
Genomes: 𝑓 0.00044 ( 0 hom., cov: 33)
Exomes 𝑓: 0.00095 ( 2 hom. )
Consequence
ACP6
NM_016361.5 missense
NM_016361.5 missense
Scores
1
4
12
Clinical Significance
Conservation
PhyloP100: 1.13
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 Uncertain_significance. Variant got 0 ACMG points.
PP5
Variant 1-147659496-C-T is Pathogenic according to our data. Variant chr1-147659496-C-T is described in ClinVar as [Likely_pathogenic]. Clinvar id is 224824.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-147659496-C-T is described in Lovd as [Likely_pathogenic].
BP4
Computational evidence support a benign effect (MetaRNN=0.10326934). . Strength limited to SUPPORTING due to the PP5.
BS2
High Homozygotes in GnomAdExome4 at 2 AR geneVariant has number of homozygotes lower than other variant known as pathogenic in the gene, so the strength is limited to Supporting.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ACP6 | NM_016361.5 | c.379G>A | p.Val127Met | missense_variant | 3/10 | ENST00000583509.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ACP6 | ENST00000583509.7 | c.379G>A | p.Val127Met | missense_variant | 3/10 | 1 | NM_016361.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000440 AC: 67AN: 152226Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.000382 AC: 96AN: 251342Hom.: 0 AF XY: 0.000375 AC XY: 51AN XY: 135852
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GnomAD4 exome AF: 0.000947 AC: 1384AN: 1461868Hom.: 2 Cov.: 42 AF XY: 0.000921 AC XY: 670AN XY: 727236
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GnomAD4 genome AF: 0.000440 AC: 67AN: 152344Hom.: 0 Cov.: 33 AF XY: 0.000403 AC XY: 30AN XY: 74498
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ClinVar
Significance: Likely pathogenic
Submissions summary: Pathogenic:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Cerebral visual impairment and intellectual disability Pathogenic:1
Likely pathogenic, criteria provided, single submitter | research | Lupski Lab, Baylor-Hopkins CMG, Baylor College of Medicine | Sep 09, 2015 | This study shows that diverse genetic causes underlie CVI. - |
Computational scores
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Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Benign
T;.;.;T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Benign
D
LIST_S2
Benign
T;T;D;D
M_CAP
Benign
T
MetaRNN
Benign
T;T;T;T
MetaSVM
Benign
T
MutationAssessor
Pathogenic
M;M;.;.
MutationTaster
Benign
D;D
PrimateAI
Benign
T
REVEL
Benign
Sift4G
Uncertain
D;D;D;D
Polyphen
D;D;.;.
Vest4
MVP
ClinPred
D
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