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11-47245528-C-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BA1

The NM_001610.4(ACP2):c.495G>A(p.Leu165=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0396 in 1,614,214 control chromosomes in the GnomAD database, including 1,695 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.034 ( 123 hom., cov: 33)
Exomes 𝑓: 0.040 ( 1572 hom. )

Consequence

ACP2
NM_001610.4 synonymous

Scores

2

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: 1.56
Variant links:
Genes affected
ACP2 (HGNC:123): (acid phosphatase 2, lysosomal) The protein encoded by this gene belongs to the histidine acid phosphatase family, which hydrolyze orthophosphoric monoesters to alcohol and phosphate. This protein is localized to the lysosomal membrane, and is chemically and genetically distinct from the red cell acid phosphatase. Mice lacking this gene showed multiple defects, including bone structure alterations, lysosomal storage defects, and an increased tendency towards seizures. An enzymatically-inactive allele of this gene in mice showed severe growth retardation, hair-follicle abnormalities, and an ataxia-like phenotype. Alternatively spliced transcript variants have been found for this gene. A C-terminally extended isoform is also predicted to be produced by the use of an alternative in-frame translation termination codon via a stop codon readthrough mechanism. [provided by RefSeq, Oct 2017]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.47).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 11-47245528-C-T is Benign according to our data. Variant chr11-47245528-C-T is described in ClinVar as [Benign]. Clinvar id is 558906.Status of the report is no_assertion_criteria_provided, 0 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=1.56 with no splicing effect.
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.11 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ACP2NM_001610.4 linkuse as main transcriptc.495G>A p.Leu165= synonymous_variant 5/11 ENST00000672073.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ACP2ENST00000672073.1 linkuse as main transcriptc.495G>A p.Leu165= synonymous_variant 5/11 NM_001610.4 P1P11117-1

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0341
AC:
5196
AN:
152208
Hom.:
125
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0226
Gnomad AMI
AF:
0.0230
Gnomad AMR
AF:
0.0167
Gnomad ASJ
AF:
0.0156
Gnomad EAS
AF:
0.0432
Gnomad SAS
AF:
0.119
Gnomad FIN
AF:
0.0465
Gnomad MID
AF:
0.0127
Gnomad NFE
AF:
0.0377
Gnomad OTH
AF:
0.0316
GnomAD3 exomes
AF:
0.0439
AC:
11045
AN:
251460
Hom.:
397
AF XY:
0.0482
AC XY:
6552
AN XY:
135906
show subpopulations
Gnomad AFR exome
AF:
0.0234
Gnomad AMR exome
AF:
0.0128
Gnomad ASJ exome
AF:
0.0124
Gnomad EAS exome
AF:
0.0383
Gnomad SAS exome
AF:
0.121
Gnomad FIN exome
AF:
0.0500
Gnomad NFE exome
AF:
0.0387
Gnomad OTH exome
AF:
0.0341
GnomAD4 exome
AF:
0.0401
AC:
58666
AN:
1461888
Hom.:
1572
Cov.:
31
AF XY:
0.0425
AC XY:
30938
AN XY:
727248
show subpopulations
Gnomad4 AFR exome
AF:
0.0234
Gnomad4 AMR exome
AF:
0.0138
Gnomad4 ASJ exome
AF:
0.0126
Gnomad4 EAS exome
AF:
0.0352
Gnomad4 SAS exome
AF:
0.113
Gnomad4 FIN exome
AF:
0.0501
Gnomad4 NFE exome
AF:
0.0364
Gnomad4 OTH exome
AF:
0.0416
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0341
AC:
5193
AN:
152326
Hom.:
123
Cov.:
33
AF XY:
0.0357
AC XY:
2662
AN XY:
74486
show subpopulations
Gnomad4 AFR
AF:
0.0228
Gnomad4 AMR
AF:
0.0166
Gnomad4 ASJ
AF:
0.0156
Gnomad4 EAS
AF:
0.0425
Gnomad4 SAS
AF:
0.118
Gnomad4 FIN
AF:
0.0465
Gnomad4 NFE
AF:
0.0377
Gnomad4 OTH
AF:
0.0318
Alfa
AF:
0.0297
Hom.:
58
Bravo
AF:
0.0289
Asia WGS
AF:
0.117
AC:
408
AN:
3478
EpiCase
AF:
0.0362
EpiControl
AF:
0.0354

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: no assertion criteria provided
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, no assertion criteria providedclinical testingMayo Clinic Laboratories, Mayo ClinicMar 16, 2017- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.47
Cadd
Benign
8.5
Dann
Benign
0.87
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7

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: rs10838677; hg19: chr11-47267079; API