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NM_003978.5(PSTPIP1):c.354+10G>A

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Interpretation:
Benign/Likely benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
5 (Most recent: Oct 15, 2021)
Last evaluated:
Dec 31, 2019
Accession:
VCV000138821.5
Variation ID:
138821
Description:
single nucleotide variant
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NM_003978.5(PSTPIP1):c.354+10G>A

Allele ID
142524
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
15q24.3
Genomic location
15: 77025614 (GRCh38) GRCh38 UCSC
15: 77317955 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
LRG_172:g.35491G>A
LRG_172t1:c.354+10G>A
NC_000015.10:g.77025614G>A
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000015.10:77025613:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
0.00020 (A)

Allele frequency
Exome Aggregation Consortium (ExAC) 0.00015
The Genome Aggregation Database (gnomAD) 0.00022
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00017
1000 Genomes Project 0.00020
The Genome Aggregation Database (gnomAD), exomes 0.00030
Trans-Omics for Precision Medicine (TOPMed) 0.00034
Links
ClinGen: CA292931
dbSNP: rs370745407
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign/Likely benign 2 criteria provided, multiple submitters, no conflicts Dec 31, 2019 RCV000320387.3
Benign 1 criteria provided, single submitter Sep 12, 2011 RCV000127631.1
Likely benign 2 no assertion criteria provided - RCV001729402.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
PSTPIP1 - - GRCh38
GRCh37
348 368

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Benign
(Sep 12, 2011)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000171210.10
Submitted: (Mar 26, 2018)
Evidence details
Comment:
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at … (more)
Likely benign
(Dec 31, 2019)
criteria provided, single submitter
Method: clinical testing
Pyogenic arthritis, pyoderma gangrenosum and acne
Allele origin: germline
Invitae
Accession: SCV001014423.2
Submitted: (Jan 29, 2020)
Evidence details
Benign
(Jan 13, 2018)
criteria provided, single submitter
Method: clinical testing
Pyogenic arthritis-pyoderma gangrenosum-acne syndrome
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000393993.3
Submitted: (Feb 20, 2020)
Evidence details
Comment:
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated … (more)
Likely benign
(-)
no assertion criteria provided
Method: clinical testing
not provided
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: SCV001978417.1
Submitted: (Oct 15, 2021)
Evidence details
Likely benign
(-)
no assertion criteria provided
Method: clinical testing
not provided
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: SCV001980287.1
Submitted: (Oct 15, 2021)
Evidence details

Functional evidence

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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 this variant

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There are no citations in ClinVar for this variation. If you know of citations for this variation, please consider submitting that information to ClinVar.

Text-mined citations for rs370745407...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Oct 16, 2021