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NM_000195.5(HPS1):c.198G>A (p.Ser66=)

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Interpretation:
Conflicting interpretations of pathogenicity​

Benign(1);Uncertain significance(3)

Review status:
criteria provided, conflicting interpretations
Submissions:
5 (Most recent: Jan 7, 2021)
Last evaluated:
Dec 7, 2020
Accession:
VCV000502551.6
Variation ID:
502551
Description:
single nucleotide variant
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NM_000195.5(HPS1):c.198G>A (p.Ser66=)

Allele ID
493975
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
10q24.2
Genomic location
10: 98435692 (GRCh38) GRCh38 UCSC
10: 100195449 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
LRG_562:g.16256G>A
NC_000010.10:g.100195449C>T
NC_000010.11:g.98435692C>T
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000010.11:98435691:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
0.00140 (T)

Allele frequency
Exome Aggregation Consortium (ExAC) 0.00028
The Genome Aggregation Database (gnomAD), exomes 0.00026
The Genome Aggregation Database (gnomAD) 0.00102
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00108
Trans-Omics for Precision Medicine (TOPMed) 0.00106
1000 Genomes Project 0.00140
Links
ClinGen: CA5639479
dbSNP: rs115265574
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Uncertain significance 2 criteria provided, multiple submitters, no conflicts Jan 25, 2019 RCV000758238.2
Conflicting interpretations of pathogenicity 2 criteria provided, conflicting interpretations Dec 7, 2020 RCV000592415.4
Likely benign 1 no assertion criteria provided Jan 13, 2020 RCV001275788.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
HPS1 - - GRCh38
GRCh37
400 419

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Uncertain significance
(Jun 14, 2017)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000709335.2
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Uncertain significance
(Jan 25, 2019)
criteria provided, single submitter
Method: clinical testing
Hermansky-Pudlak syndrome 1
Allele origin: germline
Johns Hopkins Genomics, Johns Hopkins University
Accession: SCV000886876.1
Submitted: (Mar 05, 2019)
Evidence details
Comment:
This HPS1 variant (rs115265574) has been identified in large population datasets and the minor allele frequency is neither low enough to consider the variant rare … (more)
Uncertain significance
(Jan 13, 2018)
criteria provided, single submitter
Method: clinical testing
Hermansky-Pudlak syndrome 1
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001265832.1
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)
Benign
(Dec 07, 2020)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Invitae
Accession: SCV001047014.3
Submitted: (Jan 07, 2021)
Evidence details
Likely benign
(Jan 13, 2020)
no assertion criteria provided
Method: clinical testing
Hermansky-Pudlak syndrome
Allele origin: germline
Natera, Inc.
Accession: SCV001461341.1
Submitted: (Dec 28, 2020)
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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Title Author Journal Year Link
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=HPS1 - - - -

Text-mined citations for rs115265574...

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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 Jun 14, 2021