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NM_001330078.2(NRXN1):c.2421C>T (p.Asn807=)

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Interpretation:
Benign/Likely benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
8 (Most recent: Jan 7, 2021)
Last evaluated:
Dec 2, 2020
Accession:
VCV000093591.7
Variation ID:
93591
Description:
single nucleotide variant
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NM_001330078.2(NRXN1):c.2421C>T (p.Asn807=)

Allele ID
99495
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
2p16.3
Genomic location
2: 50506571 (GRCh38) GRCh38 UCSC
2: 50733709 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000002.11:g.50733709G>A
NC_000002.11:g.50733709G>A
NC_000002.12:g.50506571G>A
... more HGVS
Protein change
-
Other names
p.N847N:AAC>AAT
Canonical SPDI
NC_000002.12:50506570:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
0.00519 (A)

Allele frequency
The Genome Aggregation Database (gnomAD) 0.00472
Trans-Omics for Precision Medicine (TOPMed) 0.00528
Exome Aggregation Consortium (ExAC) 0.00156
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00553
The Genome Aggregation Database (gnomAD), exomes 0.00124
1000 Genomes Project 0.00519
Links
ClinGen: CA147118
dbSNP: rs115211871
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign 5 criteria provided, multiple submitters, no conflicts Jan 13, 2017 RCV000079516.7
Benign 2 criteria provided, multiple submitters, no conflicts Dec 2, 2020 RCV000230396.8
Likely benign 1 criteria provided, single submitter Apr 21, 2016 RCV000715066.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
NRXN1 Sufficient evidence for dosage pathogenicity No evidence available GRCh38
GRCh37
1294 1356

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Benign
(Dec 14, 2012)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000111398.8
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Benign
(Oct 21, 2013)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000170806.9
Submitted: (Mar 26, 2018)
Evidence details
Comment:
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at … (more)
Benign
(-)
criteria provided, single submitter
Method: clinical testing
NOT SPECIFIED
Allele origin: germline
PreventionGenetics,PreventionGenetics
Accession: SCV000306817.1
Submitted: (Apr 28, 2016)
Evidence details
Benign
(Oct 20, 2015)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Genetic Services Laboratory, University of Chicago
Accession: SCV000248278.2
Submitted: (Oct 04, 2017)
Evidence details
Benign
(Jan 13, 2017)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Athena Diagnostics Inc
Accession: SCV000614359.1
Submitted: (Aug 17, 2017)
Evidence details
Benign
(Jan 12, 2018)
criteria provided, single submitter
Method: clinical testing
Pitt-Hopkins-like syndrome 2
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000431203.3
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
(Apr 21, 2016)
criteria provided, single submitter
Method: clinical testing
History of neurodevelopmental disorder
Allele origin: germline
Ambry Genetics
Accession: SCV000845890.3
Submitted: (Nov 30, 2020)
Evidence details
Comment:
In silico models in agreement (benign) ;Synonymous alterations with insufficient evidence to classify as benign
Benign
(Dec 02, 2020)
criteria provided, single submitter
Method: clinical testing
Pitt-Hopkins-like syndrome 2
Allele origin: germline
Invitae
Accession: SCV000286213.7
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=NRXN1 - - - -

Text-mined citations for rs115211871...

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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