chr1-147659496-C-T

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

Scores

1
4
12

Clinical Significance

Likely pathogenic criteria provided, single submitter P:1

Conservation

PhyloP100: 1.13
Variant links:
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]

Genome browser will be placed here

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
ACP6NM_016361.5 linkuse as main transcriptc.379G>A p.Val127Met missense_variant 3/10 ENST00000583509.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ACP6ENST00000583509.7 linkuse as main transcriptc.379G>A p.Val127Met missense_variant 3/101 NM_016361.5 P1Q9NPH0-1

Frequencies

GnomAD3 genomes
AF:
0.000440
AC:
67
AN:
152226
Hom.:
0
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.000145
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000897
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.000382
AC:
96
AN:
251342
Hom.:
0
AF XY:
0.000375
AC XY:
51
AN XY:
135852
show subpopulations
Gnomad AFR exome
AF:
0.000246
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000801
Gnomad OTH exome
AF:
0.000163
GnomAD4 exome
AF:
0.000947
AC:
1384
AN:
1461868
Hom.:
2
Cov.:
42
AF XY:
0.000921
AC XY:
670
AN XY:
727236
show subpopulations
Gnomad4 AFR exome
AF:
0.000209
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:
0.0000187
Gnomad4 NFE exome
AF:
0.00122
Gnomad4 OTH exome
AF:
0.000348
GnomAD4 genome
AF:
0.000440
AC:
67
AN:
152344
Hom.:
0
Cov.:
33
AF XY:
0.000403
AC XY:
30
AN XY:
74498
show subpopulations
Gnomad4 AFR
AF:
0.000144
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000897
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.000754
Hom.:
0
Bravo
AF:
0.000423
TwinsUK
AF:
0.00243
AC:
9
ALSPAC
AF:
0.00182
AC:
7
ESP6500AA
AF:
0.000454
AC:
2
ESP6500EA
AF:
0.00105
AC:
9
ExAC
AF:
0.000428
AC:
52
Asia WGS
AF:
0.000289
AC:
1
AN:
3478
EpiCase
AF:
0.000382
EpiControl
AF:
0.000356

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 submitterresearchLupski Lab, Baylor-Hopkins CMG, Baylor College of MedicineSep 09, 2015This study shows that diverse genetic causes underlie CVI. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.11
BayesDel_addAF
Benign
-0.40
T
BayesDel_noAF
Benign
-0.35
CADD
Uncertain
25
DANN
Uncertain
1.0
DEOGEN2
Benign
0.077
T;.;.;T
Eigen
Uncertain
0.52
Eigen_PC
Uncertain
0.48
FATHMM_MKL
Benign
0.66
D
LIST_S2
Benign
0.78
T;T;D;D
M_CAP
Benign
0.012
T
MetaRNN
Benign
0.10
T;T;T;T
MetaSVM
Benign
-0.98
T
MutationAssessor
Pathogenic
3.0
M;M;.;.
MutationTaster
Benign
1.0
D;D
PrimateAI
Benign
0.44
T
REVEL
Benign
0.18
Sift4G
Uncertain
0.0050
D;D;D;D
Polyphen
0.99
D;D;.;.
Vest4
0.44
MVP
0.40
ClinPred
0.74
D
GERP RS
4.7
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1
Varity_R
0.22
gMVP
0.48

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
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: rs144959805; hg19: chr1-147131611; API