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NM_002778.4(PSAP):c.174+9C>T

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Interpretation:
Conflicting interpretations of pathogenicity​

Benign(1);Likely benign(1);Uncertain significance(3)

Review status:
criteria provided, conflicting interpretations
Submissions:
5 (Most recent: Jan 7, 2021)
Last evaluated:
Dec 4, 2020
Accession:
VCV000300532.5
Variation ID:
300532
Description:
single nucleotide variant
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NM_002778.4(PSAP):c.174+9C>T

Allele ID
310781
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
10q22.1
Genomic location
10: 71834363 (GRCh38) GRCh38 UCSC
10: 73594120 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000010.10:g.73594120G>A
NC_000010.11:g.71834363G>A
NG_009301.1:g.21963C>T
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000010.11:71834362:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
0.00100 (A)

Allele frequency
The Genome Aggregation Database (gnomAD), exomes 0.00023
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00054
Exome Aggregation Consortium (ExAC) 0.00024
Trans-Omics for Precision Medicine (TOPMed) 0.00084
The Genome Aggregation Database (gnomAD) 0.00083
1000 Genomes Project 0.00100
Links
ClinGen: CA5547878
dbSNP: rs141133813
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign 1 criteria provided, single submitter Jan 13, 2018 RCV000307686.2
Uncertain significance 1 criteria provided, single submitter Jan 13, 2018 RCV000362343.2
Uncertain significance 1 criteria provided, single submitter Jan 13, 2018 RCV000361163.2
Conflicting interpretations of pathogenicity 2 criteria provided, conflicting interpretations Dec 4, 2020 RCV000895393.4
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
PSAP - - GRCh38
GRCh37
320 369

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Uncertain significance
(Jan 13, 2018)
criteria provided, single submitter
Method: clinical testing
Combined saposin deficiency
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000364163.3
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)
Uncertain significance
(Jan 13, 2018)
criteria provided, single submitter
Method: clinical testing
Krabbe disease, atypical, due to saposin A deficiency
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000364166.3
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)
Uncertain significance
(Jan 13, 2018)
criteria provided, single submitter
Method: clinical testing
Sphingolipid activator protein 1 deficiency
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000364164.3
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
(Jan 13, 2018)
criteria provided, single submitter
Method: clinical testing
Gaucher disease, atypical, due to saposin C deficiency
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000364165.3
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
(Dec 04, 2020)
criteria provided, single submitter
Method: clinical testing
Sphingolipid activator protein 1 deficiency
Allele origin: germline
Invitae
Accession: SCV001039430.3
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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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 rs141133813...

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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 Sep 07, 2021