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NM_024747.6(HPS6):c.1779G>A (p.Pro593=)

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Interpretation:
Benign/Likely benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
3 (Most recent: Jan 7, 2021)
Last evaluated:
Nov 24, 2020
Accession:
VCV000282222.5
Variation ID:
282222
Description:
single nucleotide variant
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NM_024747.6(HPS6):c.1779G>A (p.Pro593=)

Allele ID
266459
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
10q24.32
Genomic location
10: 102067253 (GRCh38) GRCh38 UCSC
10: 103827010 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000010.10:g.103827010G>A
NM_024747.5:c.1779G>A NP_079023.2:p.Pro593= synonymous
NC_000010.10:g.103827010G>A
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000010.11:102067252:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
0.00200 (A)

Allele frequency
Exome Aggregation Consortium (ExAC) 0.00062
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00196
1000 Genomes Project 0.00200
The Genome Aggregation Database (gnomAD) 0.00204
Trans-Omics for Precision Medicine (TOPMed) 0.00205
The Genome Aggregation Database (gnomAD), exomes 0.00054
Links
ClinGen: CA5660034
dbSNP: rs77529785
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely benign 1 criteria provided, single submitter Jan 13, 2018 RCV000283876.2
Benign 1 criteria provided, single submitter Sep 11, 2015 RCV000306350.1
Benign 1 criteria provided, single submitter Nov 24, 2020 RCV000906398.3
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
HPS6 - - GRCh38
GRCh37
110 125

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Benign
(Sep 11, 2015)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000333567.4
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Likely benign
(Jan 13, 2018)
criteria provided, single submitter
Method: clinical testing
Hermansky-Pudlak syndrome 6
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000360071.3
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)
Benign
(Nov 24, 2020)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Invitae
Accession: SCV001051032.3
Submitted: (Jan 07, 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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Title Author Journal Year Link
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=HPS6 - - - -

Text-mined citations for rs77529785...

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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 24, 2021