ClinVar Genomic variation as it relates to human health
NM_001611.5(ACP5):c.814C>T (p.Arg272Cys)
The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.
Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.
Uncertain significance(2); Benign(3); Likely benign(3)
No data submitted for somatic clinical impact
No data submitted for oncogenicity
Variant Details
- Identifiers
-
NM_001611.5(ACP5):c.814C>T (p.Arg272Cys)
Variation ID: 198455 Accession: VCV000198455.50
- Type and length
-
single nucleotide variant, 1 bp
- Location
-
Cytogenetic: 19p13.2 19: 11575174 (GRCh38) [ NCBI UCSC ] 19: 11685989 (GRCh37) [ NCBI UCSC ]
- Timeline in ClinVar
-
First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.
Last submission Help The date of the most recent submission for each type of classification for this variant.
Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline Jun 28, 2015 Aug 4, 2024 Jan 29, 2024 - HGVS
-
Nucleotide Protein Molecular
consequenceNM_001611.5:c.814C>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_001602.1:p.Arg272Cys missense NM_001111034.3:c.814C>T NP_001104504.1:p.Arg272Cys missense NM_001111035.3:c.814C>T NP_001104505.1:p.Arg272Cys missense NM_001111036.3:c.814C>T NP_001104506.1:p.Arg272Cys missense NM_001322023.2:c.814C>T NP_001308952.1:p.Arg272Cys missense NC_000019.10:g.11575174G>A NC_000019.9:g.11685989G>A NG_028127.1:g.8813C>T LRG_1218:g.8813C>T LRG_1218t1:c.814C>T LRG_1218p1:p.Arg272Cys - Protein change
- R272C
- Other names
- -
- Canonical SPDI
- NC_000019.10:11575173:G:A
-
Functional
consequence HelpThe effect of the variant on RNA or protein function, based on experimental evidence from submitters.
-
-
Global minor allele
frequency (GMAF) HelpThe global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.
-
0.00200 (A)
-
Allele frequency
Help
The frequency of the allele represented by this VCV record.
1000 Genomes Project 0.00200
1000 Genomes Project 30x 0.00203
Trans-Omics for Precision Medicine (TOPMed) 0.00333
The Genome Aggregation Database (gnomAD) 0.00338
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00438
Genes
Gene | OMIM | ClinGen Gene Dosage Sensitivity Curation |
Variation Viewer
Help
Links to Variation Viewer, a genome browser to view variation data from NCBI databases. |
Related variants | ||
---|---|---|---|---|---|---|
HI score
Help
The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
TS score
Help
The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
Within gene
Help
The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants. |
All
Help
The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene. |
|||
ACP5 | - | - |
GRCh38 GRCh37 |
299 | 317 |
Conditions - Germline
Condition
Help
The condition for this variant-condition (RCV) record in ClinVar. |
Classification
Help
The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions) |
Review status
Help
The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. |
Last evaluated
Help
The most recent date that a submitter evaluated this variant for the condition. |
Variation/condition record
Help
The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page. |
---|---|---|---|---|
Benign (2) |
criteria provided, multiple submitters, no conflicts
|
Mar 17, 2017 | RCV000179812.11 | |
Conflicting interpretations of pathogenicity (6) |
criteria provided, conflicting classifications
|
Mar 1, 2023 | RCV000514245.31 | |
Conflicting interpretations of pathogenicity (2) |
criteria provided, conflicting classifications
|
Jan 29, 2024 | RCV000537794.15 | |
ACP5-related disorder
|
Likely benign (1) |
criteria provided, single submitter
|
May 3, 2022 | RCV003955090.1 |
Submissions - Germline
Classification
Help
The submitted germline classification for each SCV record. (Last evaluated) |
Review status
Help
Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria) |
Condition
Help
The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant. |
Submitter
Help
The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar. |
More information
Help
This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter. |
|
---|---|---|---|---|---|
Likely benign
(Jun 12, 2017)
|
criteria provided, single submitter
Method: clinical testing
|
not provided
Affected status: not provided
Allele origin:
germline
|
Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics
Accession: SCV000610007.1
First in ClinVar: Nov 05, 2017 Last updated: Nov 05, 2017 |
|
|
Benign
(May 01, 2015)
|
criteria provided, single submitter
Method: clinical testing
|
not specified
Affected status: unknown
Allele origin:
germline
|
Eurofins Ntd Llc (ga)
Accession: SCV000232120.5
First in ClinVar: Jun 28, 2015 Last updated: Jun 28, 2015 |
Sex: mixed
|
|
Benign
(Jan 29, 2024)
|
criteria provided, single submitter
Method: clinical testing
|
Spondyloenchondrodysplasia with immune dysregulation
Affected status: unknown
Allele origin:
germline
|
Labcorp Genetics (formerly Invitae), Labcorp
Accession: SCV000639587.8
First in ClinVar: Dec 26, 2017 Last updated: Feb 20, 2024 |
|
|
Benign
(Mar 17, 2017)
|
criteria provided, single submitter
Method: clinical testing
|
Not Specified
Affected status: unknown
Allele origin:
germline
|
Institute for Genomic Medicine (IGM) Clinical Laboratory, Nationwide Children's Hospital
Accession: SCV000864307.1
First in ClinVar: Jan 22, 2019 Last updated: Jan 22, 2019 |
Comment:
BS1, BS2, BP6; This alteration has an allele frequency that is greater than expected for the associated disease, was seen in a healthy adult where … (more)
BS1, BS2, BP6; This alteration has an allele frequency that is greater than expected for the associated disease, was seen in a healthy adult where full penetrance of the disorder is expected at an early age, and was reported as a benign/likely benign alteration by a reputable source (ClinVar or other correspondence from a clinical testing laboratory). (less)
|
|
Uncertain significance
(Apr 04, 2022)
|
criteria provided, single submitter
Method: clinical testing
|
Not Provided
Affected status: yes
Allele origin:
germline
|
GeneDx
Accession: SCV001993674.3
First in ClinVar: Nov 05, 2021 Last updated: Mar 04, 2023 |
Comment:
Has not been previously published as pathogenic or benign to our knowledge; In silico analysis supports that this missense variant has a deleterious effect on … (more)
Has not been previously published as pathogenic or benign to our knowledge; In silico analysis supports that this missense variant has a deleterious effect on protein structure/function (less)
|
|
Uncertain significance
(Nov 23, 2021)
|
criteria provided, single submitter
Method: clinical testing
|
Spondyloenchondrodysplasia with immune dysregulation
Affected status: unknown
Allele origin:
germline
|
Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago
Accession: SCV000898501.2
First in ClinVar: Apr 25, 2019 Last updated: May 06, 2023 |
Comment:
ACP5 NM_001111035.2 exon 7 p.Arg272Cys (c.814C>T): This variant has not been reported in the literature but is present in 0.4% (595/126376) of European alleles, including … (more)
ACP5 NM_001111035.2 exon 7 p.Arg272Cys (c.814C>T): This variant has not been reported in the literature but is present in 0.4% (595/126376) of European alleles, including 3 homozygotes, in the Genome Aggregation Database (http://gnomad.broadinstitute.org/variant/19-11685989-G-A). This variant is present in ClinVar, with several labs classifying this variant as likely benign or benign (Variation ID:198455). Evolutionary conservation and computational predictive tools for this variant are unclear. In summary, data on this variant is insufficient for disease classification. Therefore, the clinical significance of this variant is uncertain. (less)
|
|
Likely benign
(May 03, 2022)
|
criteria provided, single submitter
Method: clinical testing
|
ACP5-related condition
Affected status: unknown
Allele origin:
germline
|
PreventionGenetics, part of Exact Sciences
Accession: SCV004769636.1
First in ClinVar: Mar 16, 2024 Last updated: Mar 16, 2024 |
Comment:
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications).
|
|
Likely benign
(Mar 01, 2023)
|
criteria provided, single submitter
Method: clinical testing
|
not provided
Affected status: yes
Allele origin:
germline
|
CeGaT Center for Human Genetics Tuebingen
Accession: SCV001246014.24
First in ClinVar: May 12, 2020 Last updated: Aug 04, 2024 |
Comment:
ACP5: BP4, BS2
Number of individuals with the variant: 4
|
|
Likely benign
(-)
|
no assertion criteria provided
Method: clinical testing
|
not provided
Affected status: yes
Allele origin:
germline
|
Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC)
Study: VKGL Data-share Consensus
Accession: SCV001799199.1 First in ClinVar: Aug 21, 2021 Last updated: Aug 21, 2021 |
|
|
Likely benign
(-)
|
no assertion criteria provided
Method: clinical testing
|
not provided
Affected status: yes
Allele origin:
germline
|
Genome Diagnostics Laboratory, University Medical Center Utrecht
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001931762.1 First in ClinVar: Sep 24, 2021 Last updated: Sep 24, 2021 |
|
|
Likely benign
(-)
|
no assertion criteria provided
Method: clinical testing
|
not provided
Affected status: yes
Allele origin:
germline
|
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001963823.1 First in ClinVar: Oct 07, 2021 Last updated: Oct 07, 2021 |
|
|
click to load more click to collapse |
Germline Functional Evidence
There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar. |
Citations for germline classification of this variant
HelpTitle | Author | Journal | Year | Link |
---|---|---|---|---|
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=ACP5 | - | - | - | - |
Text-mined citations for rs147025508 ...
HelpRecord last updated Sep 29, 2024
This date represents the last time this VCV record was updated. The update may be due to an update to one of the included submitted records (SCVs), or due to an update that ClinVar made to the variant such as adding HGVS expressions or a rs number. So this date may be different from the date of the “most recent submission” reported at the top of this page.