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NM_001365999.1(SZT2):c.759G>A (p.Ser253=)

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Interpretation:
Benign/Likely benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
4 (Most recent: Sep 15, 2021)
Last evaluated:
Dec 2, 2020
Accession:
VCV000416979.9
Variation ID:
416979
Description:
single nucleotide variant
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NM_001365999.1(SZT2):c.759G>A (p.Ser253=)

Allele ID
391220
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
1p34.2
Genomic location
1: 43416088 (GRCh38) GRCh38 UCSC
1: 43881759 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000001.10:g.43881759G>A
NC_000001.11:g.43416088G>A
NG_029091.1:g.31204G>A
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000001.11:43416087:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
0.00539 (A)

Allele frequency
The Genome Aggregation Database (gnomAD), exomes 0.00187
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00732
The Genome Aggregation Database (gnomAD) 0.00768
Exome Aggregation Consortium (ExAC) 0.00203
1000 Genomes Project 0.00539
The Genome Aggregation Database (gnomAD) 0.00663
Trans-Omics for Precision Medicine (TOPMed) 0.00783
Trans-Omics for Precision Medicine (TOPMed) 0.00816
Links
ClinGen: CA808258
dbSNP: rs1889586
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign 3 criteria provided, multiple submitters, no conflicts Dec 2, 2020 RCV000713759.7
Likely benign 1 criteria provided, single submitter Mar 18, 2016 RCV000716173.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
SZT2 - - GRCh38
GRCh37
1540 1651

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Benign
(Mar 05, 2018)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Athena Diagnostics Inc
Accession: SCV000844388.1
Submitted: (Aug 31, 2018)
Evidence details
Likely benign
(Mar 18, 2016)
criteria provided, single submitter
Method: clinical testing
Seizures
Allele origin: germline
Ambry Genetics
Accession: SCV000847010.2
Submitted: (Nov 30, 2020)
Evidence details
Comment:
Synonymous alterations with insufficient evidence to classify as benign
Benign
(Dec 02, 2020)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Invitae
Accession: SCV000563183.5
Submitted: (Jan 07, 2021)
Evidence details
Benign
(Oct 11, 2019)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV001873157.1
Submitted: (Sep 15, 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 rs1889586...

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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