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dbSNP Short Genetic Variations

Reference SNP (rs) Report

This page reports data for a single dbSNP Reference SNP variation (RefSNP or rs) from the new redesigned dbSNP build.
Top of the page reports a concise summary for the rs, with more specific details included in the corresponding tabs below.
All alleles are reported in the Forward orientation. Use the Genomic View to inspect the nucleotides flanking the variant, and its neighbors.
For more information see Help documentation.

rs121913502

Current Build 153

Released July 9, 2019

Organism
Homo sapiens
Position
chr15:90088702 (GRCh38.p12) Help

The anchor position for this RefSNP. Includes all nucleotides potentially affected by this change, thus it can differ from HGVS, which is right-shifted. See here for details.

Alleles
C>A / C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.00003 (8/251462, GnomAD_exome)
T=0.00010 (12/121404, ExAC)
Clinical Significance
Reported in ClinVar
Gene : Consequence
IDH2 : Missense Variant
Publications
14 citations
Genomic View
See rs on genome
Help

Variant Details tab shows known variant placements on genomic sequences: chromosomes (NC_), RefSeqGene, pseudogenes or genomic regions (NG_), and in a separate table: on transcripts (NM_) and protein sequences (NP_). The corresponding transcript and protein locations are listed in adjacent lines, along with molecular consequences from Sequence Ontology. When no protein placement is available, only the transcript is listed. Column "Codon[Amino acid]" shows the actual base change in the format of "Reference > Alternate" allele, including the nucleotide codon change in transcripts, and the amino acid change in proteins, respectively, allowing for known ribosomal slippage sites. To view nucleotides adjacent to the variant use the Genomic View at the bottom of the page - zoom into the sequence until the nucleotides around the variant become visible.

Genomic Placements
Sequence name Change
GRCh38.p12 chr 15 NC_000015.10:g.90088702C>A
GRCh38.p12 chr 15 NC_000015.10:g.90088702C>T
GRCh37.p13 chr 15 NC_000015.9:g.90631934C>A
GRCh37.p13 chr 15 NC_000015.9:g.90631934C>T
NADP(+ RefSeqGene (LRG_611) NG_023302.1:g.18775G>T
NADP(+ RefSeqGene (LRG_611) NG_023302.1:g.18775G>A
Gene: IDH2, isocitrate dehydrogenase (NADP(+)) 2, mitochondrial (minus strand)
Molecule type Change Amino acid[Codon] SO Term
IDH2 transcript variant 2 NM_001289910.1:c.263G>T R [CGG] > L [CTG] Coding Sequence Variant
isocitrate dehydrogenase [NADP], mitochondrial isoform 2 NP_001276839.1:p.Arg88Leu R (Arg) > L (Leu) Missense Variant
IDH2 transcript variant 2 NM_001289910.1:c.263G>A R [CGG] > Q [CAG] Coding Sequence Variant
isocitrate dehydrogenase [NADP], mitochondrial isoform 2 NP_001276839.1:p.Arg88Gln R (Arg) > Q (Gln) Missense Variant
IDH2 transcript variant 1 NM_002168.3:c.419G>T R [CGG] > L [CTG] Coding Sequence Variant
isocitrate dehydrogenase [NADP], mitochondrial isoform 1 precursor NP_002159.2:p.Arg140Leu R (Arg) > L (Leu) Missense Variant
IDH2 transcript variant 1 NM_002168.3:c.419G>A R [CGG] > Q [CAG] Coding Sequence Variant
isocitrate dehydrogenase [NADP], mitochondrial isoform 1 precursor NP_002159.2:p.Arg140Gln R (Arg) > Q (Gln) Missense Variant
IDH2 transcript variant 3 NM_001290114.2:c.29G>T R [CGG] > L [CTG] Coding Sequence Variant
isocitrate dehydrogenase [NADP], mitochondrial isoform 3 NP_001277043.1:p.Arg10Leu R (Arg) > L (Leu) Missense Variant
IDH2 transcript variant 3 NM_001290114.2:c.29G>A R [CGG] > Q [CAG] Coding Sequence Variant
isocitrate dehydrogenase [NADP], mitochondrial isoform 3 NP_001277043.1:p.Arg10Gln R (Arg) > Q (Gln) Missense Variant
Help

Clinical Significance tab shows a list of clinical significance entries from ClinVar associated with the variation, per allele. Click on the RCV accession (i.e. RCV000001615.2) or Allele ID (i.e. 12274) to access full ClinVar report.

Allele: A (allele ID: 362867 )
ClinVar Accession Disease Names Clinical Significance
RCV000419881.1 Myelodysplastic syndrome Likely-Pathogenic
RCV000424921.1 Acute myeloid leukemia Pathogenic
RCV000426646.1 Squamous cell carcinoma of the head and neck Likely-Pathogenic
RCV000435643.1 Multiple myeloma Likely-Pathogenic
RCV000436884.1 Neoplasm of the large intestine Likely-Pathogenic
Allele: T (allele ID: 29755 )
ClinVar Accession Disease Names Clinical Significance
RCV000015831.27 D-2-hydroxyglutaric aciduria 2 Pathogenic
RCV000292094.1 not provided Pathogenic
RCV000419192.1 Acute myeloid leukemia Pathogenic
RCV000420290.1 Squamous cell carcinoma of the head and neck Likely-Pathogenic
RCV000430530.1 Neoplasm of the large intestine Likely-Pathogenic
RCV000431189.1 Myelodysplastic syndrome Likely-Pathogenic
RCV000441454.1 Multiple myeloma Likely-Pathogenic
Help

Frequency tab displays a table of the reference and alternate allele frequencies reported by various studies and populations. Table lines, where Population="Global" refer to the entire study population, whereas lines, where Group="Sub", refer to a study-specific population subgroupings (i.e. AFR, CAU, etc.), if available. Frequency for the alternate allele (Alt Allele) is a ratio of samples observed-to-total, where the numerator (observed samples) is the number of chromosomes in the study with the minor allele present (found in "Sample size", where Group="Sub"), and the denominator (total samples) is the total number of all chromosomes in the study for the variant (found in "Sample size", where Group="Study-wide" and Population="Global").

Download
Study Population Group Sample Size Ref Allele Alt Allele
gnomAD - Exomes Global Study-wide 251462 C=0.99997 T=0.00003
gnomAD - Exomes European Sub 135404 C=0.99996 T=0.00004
gnomAD - Exomes Asian Sub 49002 C=1.0000 T=0.0000
gnomAD - Exomes American Sub 34590 C=1.0000 T=0.0000
gnomAD - Exomes African Sub 16246 C=0.9999 T=0.0001
gnomAD - Exomes Ashkenazi Jewish Sub 10080 C=1.0000 T=0.0000
gnomAD - Exomes Other Sub 6140 C=1.000 T=0.000
ExAC Global Study-wide 121404 C=0.99990 T=0.00010
ExAC Europe Sub 73346 C=0.9999 T=0.0001
ExAC Asian Sub 25166 C=0.9999 T=0.0001
ExAC American Sub 11578 C=1.0000 T=0.0000
ExAC African Sub 10406 C=0.9997 T=0.0003
ExAC Other Sub 908 C=1.00 T=0.00
Help

Aliases tab displays HGVS names representing the variant placements and allele changes on genomic, transcript and protein sequences, per allele. HGVS name is an expression for reporting sequence accession and version, sequence type, position, and allele change. The column "Note" can have two values: "diff" means that there is a difference between the reference allele (variation interval) at the placement reported in HGVS name and the reference alleles reported in other HGVS names, and "rev" means that the sequence of this variation interval at the placement reported in HGVS name is in reverse orientation to the sequence(s) of this variation in other HGVS names not labeled as "rev".

Placement C= A T Note
GRCh38.p12 chr 15 NC_000015.10:g.90...

NC_000015.10:g.90088702=

NC_000015.10:g.90...

NC_000015.10:g.90088702C>A

NC_000015.10:g.90...

NC_000015.10:g.90088702C>T

GRCh37.p13 chr 15 NC_000015.9:g.906...

NC_000015.9:g.90631934=

NC_000015.9:g.906...

NC_000015.9:g.90631934C>A

NC_000015.9:g.906...

NC_000015.9:g.90631934C>T

NADP(+ RefSeqGene (LRG_611) NG_023302.1:g.18775= NG_023302.1:g.187...

NG_023302.1:g.18775G>T

NG_023302.1:g.187...

NG_023302.1:g.18775G>A

IDH2 transcript variant 1 NM_002168.3:c.419= NM_002168.3:c.419G>T NM_002168.3:c.419G>A
IDH2 transcript variant 1 NM_002168.2:c.419= NM_002168.2:c.419G>T NM_002168.2:c.419G>A
IDH2 transcript variant 3 NM_001290114.2:c.29= NM_001290114.2:c....

NM_001290114.2:c.29G>T

NM_001290114.2:c....

NM_001290114.2:c.29G>A

IDH2 transcript variant 3 NM_001290114.1:c.29= NM_001290114.1:c....

NM_001290114.1:c.29G>T

NM_001290114.1:c....

NM_001290114.1:c.29G>A

IDH2 transcript variant 2 NM_001289910.1:c....

NM_001289910.1:c.263=

NM_001289910.1:c....

NM_001289910.1:c.263G>T

NM_001289910.1:c....

NM_001289910.1:c.263G>A

isocitrate dehydrogenase [NADP], mitochondrial isoform 1 precursor NP_002159.2:p.Arg...

NP_002159.2:p.Arg140=

NP_002159.2:p.Arg...

NP_002159.2:p.Arg140Leu

NP_002159.2:p.Arg...

NP_002159.2:p.Arg140Gln

isocitrate dehydrogenase [NADP], mitochondrial isoform 3 NP_001277043.1:p....

NP_001277043.1:p.Arg10=

NP_001277043.1:p....

NP_001277043.1:p.Arg10Leu

NP_001277043.1:p....

NP_001277043.1:p.Arg10Gln

isocitrate dehydrogenase [NADP], mitochondrial isoform 2 NP_001276839.1:p....

NP_001276839.1:p.Arg88=

NP_001276839.1:p....

NP_001276839.1:p.Arg88Leu

NP_001276839.1:p....

NP_001276839.1:p.Arg88Gln

Help

Submissions tab displays variations originally submitted to dbSNP, now supporting this RefSNP cluster (rs). We display Submitter handle, Submission identifier, Date and Build number, when the submission appeared for the first time. Direct submissions to dbSNP have Submission ID in the form of an ss-prefixed number (ss#). Other supporting variations are listed in the table without ss#.

15 SubSNP, 2 Frequency, 12 ClinVar submissions
No Submitter Submission ID Date (Build)
1 DF-BWCC ss275515383 Nov 22, 2010 (133)
2 NCBI-CURATED-RECORDS ss537713266 Jan 04, 2013 (137)
3 EVA_EXAC ss1691994698 Apr 01, 2015 (144)
4 EVA_DECODE ss1696098217 Apr 01, 2015 (144)
5 CLINVAR ss2137497964 Apr 13, 2017 (150)
6 CLINVAR ss2137504363 Apr 18, 2017 (150)
7 HUMAN_LONGEVITY ss2209012497 Dec 20, 2016 (150)
8 GNOMAD ss2741506964 Nov 08, 2017 (151)
9 GNOMAD ss2749384453 Nov 08, 2017 (151)
10 GNOMAD ss2938072207 Nov 08, 2017 (151)
11 AFFY ss2985051139 Nov 08, 2017 (151)
12 TOPMED ss3234934999 Nov 08, 2017 (151)
13 ILLUMINA ss3653823152 Oct 12, 2018 (152)
14 EVA_DECODE ss3698435727 Jul 13, 2019 (153)
15 ILLUMINA ss3725523986 Jul 13, 2019 (153)
16 ExAC NC_000015.9 - 90631934 Oct 12, 2018 (152)
17 gnomAD - Exomes NC_000015.9 - 90631934 Jul 13, 2019 (153)
18 ClinVar RCV000015831.27 Oct 12, 2018 (152)
19 ClinVar RCV000292094.1 Oct 12, 2018 (152)
20 ClinVar RCV000419192.1 Oct 12, 2018 (152)
21 ClinVar RCV000419881.1 Oct 12, 2018 (152)
22 ClinVar RCV000420290.1 Oct 12, 2018 (152)
23 ClinVar RCV000424921.1 Oct 12, 2018 (152)
24 ClinVar RCV000426646.1 Oct 12, 2018 (152)
25 ClinVar RCV000430530.1 Oct 12, 2018 (152)
26 ClinVar RCV000431189.1 Oct 12, 2018 (152)
27 ClinVar RCV000435643.1 Oct 12, 2018 (152)
28 ClinVar RCV000436884.1 Oct 12, 2018 (152)
29 ClinVar RCV000441454.1 Oct 12, 2018 (152)
Help

History tab displays RefSNPs (Associated ID) from previous builds (Build) that now support the current RefSNP, and the dates, when the history was updated for each Associated ID (History Updated).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
RCV000419881.1, RCV000424921.1, RCV000426646.1, RCV000435643.1, RCV000436884.1, ss2137497964, ss2137504363 NC_000015.10:90088701:C:A NC_000015.10:90088701:C:A (self)
ss1696098217 NC_000015.8:88432937:C:T NC_000015.10:90088701:C:T (self)
2380707, 10775999, ss1691994698, ss2741506964, ss2749384453, ss2938072207, ss2985051139, ss3653823152 NC_000015.9:90631933:C:T NC_000015.10:90088701:C:T (self)
RCV000015831.27, RCV000292094.1, RCV000419192.1, RCV000420290.1, RCV000430530.1, RCV000431189.1, RCV000441454.1, ss275515383, ss537713266, ss2209012497, ss3234934999, ss3698435727, ss3725523986 NC_000015.10:90088701:C:T NC_000015.10:90088701:C:T (self)
Help

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

14 citations for rs121913502
PMID Title Author Year Journal
20171147 The common feature of leukemia-associated IDH1 and IDH2 mutations is a neomorphic enzyme activity converting alpha-ketoglutarate to 2-hydroxyglutarate. Ward PS et al. 2010 Cancer cell
20847235 IDH2 mutations in patients with D-2-hydroxyglutaric aciduria. Kranendijk M et al. 2010 Science (New York, N.Y.)
20946881 IDH1 and IDH2 mutations are frequent in Chinese patients with acute myeloid leukemia but rare in other types of hematological disorders. Zou Y et al. 2010 Biochemical and biophysical research communications
22160010 Impact of genetic features on treatment decisions in AML. Döhner H et al. 2011 Hematology. American Society of Hematology. Education Program
22397365 Molecular alterations of isocitrate dehydrogenase 1 and 2 (IDH1 and IDH2) metabolic genes and additional genetic mutations in newly diagnosed acute myeloid leukemia patients. Chotirat S et al. 2012 Journal of hematology & oncology
22417203 Prognostic relevance of integrated genetic profiling in acute myeloid leukemia. Patel JP et al. 2012 The New England journal of medicine
23558173 Targeted inhibition of mutant IDH2 in leukemia cells induces cellular differentiation. Wang F et al. 2013 Science (New York, N.Y.)
23815907 [Mutation of isocitrate dehydrogenase 2 (IDH2) gene in Chinese AML patients and its clinical significance]. Shang Z et al. 2013 Zhongguo shi yan xue ye xue za zhi
23949315 Rapid detection of IDH2 (R140Q and R172K) mutations in acute myeloid leukemia. Ashraf S et al. 2013 Annals of hematology
24049096 Novel cases of D-2-hydroxyglutaric aciduria with IDH1 or IDH2 mosaic mutations identified by amplicon deep sequencing. Nota B et al. 2013 Journal of medical genetics
24606448 Molecular evaluation of DNMT3A and IDH1/2 gene mutation: frequency, distribution pattern and associations with additional molecular markers in normal karyotype Indian acute myeloid leukemia patients. Ahmad F et al. 2014 Asian Pacific journal of cancer prevention
25157968 Prospective enterprise-level molecular genotyping of a cohort of cancer patients. MacConaill LE et al. 2014 The Journal of molecular diagnostics
25741868 Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Richards S et al. 2015 Genetics in medicine
26619011 Identifying recurrent mutations in cancer reveals widespread lineage diversity and mutational specificity. Chang MT et al. 2016 Nature biotechnology

Genomic regions, transcripts, and products
Top Help

NCBI Graphical Sequence Viewer display of the genomic region, transcripts and protein products for the reported RefSNP (rs).
Use the zoom option to view the nucleotides around the RefSNP and find other neighboring RefSNPs.
Visit Sequence Viewer for help with navigating inside the display and modifying the selection of displayed data tracks.

Software version is: 2.0.1.post246+3cda961