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NM_002485.4(NBN):c.1870C>T (p.Arg624Cys)

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely benign(1);Uncertain significance(2)

Review status:
criteria provided, conflicting interpretations
Submissions:
3 (Most recent: Jun 11, 2021)
Last evaluated:
Jan 6, 2021
Accession:
VCV000485910.8
Variation ID:
485910
Description:
single nucleotide variant
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NM_002485.4(NBN):c.1870C>T (p.Arg624Cys)

Allele ID
474908
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
8q21.3
Genomic location
8: 89947868 (GRCh38) GRCh38 UCSC
8: 90960096 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000008.10:g.90960096G>A
NC_000008.11:g.89947868G>A
NM_001024688.2:c.1624C>T NP_001019859.1:p.Arg542Cys missense
... more HGVS
Protein change
R624C, R542C
Other names
-
Canonical SPDI
NC_000008.11:89947867:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
-
Links
ClinGen: CA181275404
dbSNP: rs962092255
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Uncertain significance 1 criteria provided, single submitter Sep 24, 2020 RCV000687082.3
Conflicting interpretations of pathogenicity 2 criteria provided, conflicting interpretations Jan 6, 2021 RCV000565273.5
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
NBN Sufficient evidence for dosage pathogenicity No evidence available GRCh38
GRCh37
2221 2331

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely benign
(Dec 03, 2018)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Ambry Genetics
Accession: SCV000674011.3
Submitted: (Nov 30, 2020)
Evidence details
Comment:
In silico models in agreement (benign);Other strong data supporting benign classification
Uncertain significance
(Sep 24, 2020)
criteria provided, single submitter
Method: clinical testing
Microcephaly, normal intelligence and immunodeficiency
Allele origin: germline
Invitae
Accession: SCV000814633.3
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (1)
Comment:
This sequence change replaces arginine with cysteine at codon 624 of the NBN protein (p.Arg624Cys). The arginine residue is weakly conserved and there is a … (more)
Uncertain significance
(Jan 06, 2021)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Color Health, Inc
Accession: SCV000690679.4
Submitted: (Jun 11, 2021)
Evidence details
Comment:
This missense variant replaces arginine with cysteine at codon 624 of the NBN protein. Computational prediction suggests that this variant may not impact protein structure … (more)

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
Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. Nykamp K Genetics in medicine : official journal of the American College of Medical Genetics 2017 PMID: 28492532

Text-mined citations for rs962092255...

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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 19, 2021