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NM_000433.3(NCF2):c.1360C>T (p.Pro454Ser)

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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:
Dec 2, 2020
Accession:
VCV000294076.5
Variation ID:
294076
Description:
single nucleotide variant
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NM_000433.3(NCF2):c.1360C>T (p.Pro454Ser)

Allele ID
277863
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
1q25.3
Genomic location
1: 183560204 (GRCh38) GRCh38 UCSC
1: 183529339 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000001.10:g.183529339G>A
NC_000001.11:g.183560204G>A
NM_001127651.3:c.1360C>T NP_001121123.1:p.Pro454Ser missense
... more HGVS
Protein change
P454S, P373S, P409S
Other names
-
Canonical SPDI
NC_000001.11:183560203:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
0.00280 (A)

Allele frequency
The Genome Aggregation Database (gnomAD) 0.00401
Exome Aggregation Consortium (ExAC) 0.00412
Trans-Omics for Precision Medicine (TOPMed) 0.00471
1000 Genomes Project 0.00280
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00554
Links
ClinGen: CA1284603
dbSNP: rs55761650
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 2, 2020 RCV000551931.6
Likely benign 1 criteria provided, single submitter Dec 1, 2016 RCV000598123.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
NCF2 - - GRCh38
GRCh37
215 241

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely benign
(Dec 01, 2016)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000703533.2
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
Chronic granulomatous disease, autosomal recessive cytochrome b-positive, type 2
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000351753.3
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
(Dec 02, 2020)
criteria provided, single submitter
Method: clinical testing
Chronic granulomatous disease, autosomal recessive cytochrome b-positive, type 2
Allele origin: germline
Invitae
Accession: SCV000641908.5
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=NCF2 - - - -

Text-mined citations for rs55761650...

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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