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NM_022455.5(NSD1):c.339C>T (p.Cys113=)

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Interpretation:
Benign/Likely benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
6 (Most recent: Jan 7, 2021)
Last evaluated:
Sep 6, 2020
Accession:
VCV000159308.7
Variation ID:
159308
Description:
single nucleotide variant
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NM_022455.5(NSD1):c.339C>T (p.Cys113=)

Allele ID
168110
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
5q35.3
Genomic location
5: 177135442 (GRCh38) GRCh38 UCSC
5: 176562443 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000005.10:g.177135442C>T
NG_009821.1:g.7364C>T
NM_022455.5:c.339C>T MANE Select NP_071900.2:p.Cys113= synonymous
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000005.10:177135441:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
0.01058 (T)

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00128
The Genome Aggregation Database (gnomAD) 0.00213
Exome Aggregation Consortium (ExAC) 0.00492
The Genome Aggregation Database (gnomAD) 0.00108
Trans-Omics for Precision Medicine (TOPMed) 0.00206
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00008
The Genome Aggregation Database (gnomAD), exomes 0.00472
1000 Genomes Project 0.01058
Links
ClinGen: CA172801
dbSNP: rs77093936
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 4 criteria provided, multiple submitters, no conflicts Jan 17, 2018 RCV000146811.6
Benign 1 criteria provided, single submitter Sep 6, 2020 RCV000469195.5
Benign 1 criteria provided, single submitter Jan 25, 2017 RCV000719561.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
NSD1 Sufficient evidence for dosage pathogenicity No evidence available GRCh38
GRCh37
1090 1150

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely benign
(Feb 08, 2013)
criteria provided, single submitter
Method: clinical testing
not specified
(Autosomal dominant inheritance)
Allele origin: germline
Genetic Services Laboratory,University of Chicago
Accession: SCV000194138.1
Submitted: (Sep 11, 2014)
Evidence details
Benign
(-)
criteria provided, single submitter
Method: clinical testing
NOT SPECIFIED
Allele origin: germline
PreventionGenetics,PreventionGenetics
Accession: SCV000314061.1
Submitted: (Apr 28, 2016)
Evidence details
Benign
(Sep 04, 2014)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000227511.5
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
http://www.ncbi.nlm.nih.gov/vari…
Benign
(Jan 17, 2018)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000715066.1
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
(Jan 25, 2017)
criteria provided, single submitter
Method: clinical testing
History of neurodevelopmental disorder
Allele origin: germline
Ambry Genetics
Accession: SCV000850430.3
Submitted: (Nov 30, 2020)
Evidence details
Comment:
General population or subpopulation frequency is too high to be a pathogenic mutation based on disease/syndrome prevalence and penetrance
Benign
(Sep 06, 2020)
criteria provided, single submitter
Method: clinical testing
Sotos syndrome 1
Allele origin: germline
Invitae
Accession: SCV000558218.6
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.

Text-mined citations for rs77093936...

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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 Nov 27, 2021