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dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

All alleles are reported in the Forward orientation. Click on the Variant Details tab for details on Genomic Placement, Gene, and Amino Acid changes. HGVS names are in the HGVS tab.

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.

rs202247806

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr13:40793270 (GRCh38.p14) 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=0.000008 (2/264690, TOPMED)
T=0.000004 (1/250614, GnomAD_exome)
T=0.000007 (1/140210, GnomAD) (+ 3 more)
A=0.00001 (1/78698, PAGE_STUDY)
A=0.00000 (0/14708, ALFA)
T=0.00000 (0/14708, ALFA)
Clinical Significance
Reported in ClinVar
Gene : Consequence
SLC25A15 : Missense Variant
Publications
1 citation
Genomic View
See rs on genome

ALFA Allele Frequency
The ALFA project provide aggregate allele frequency from dbGaP. More information is available on the project page including descriptions, data access, and terms of use.

Release Version: 20230706150541
Population Group Sample Size Ref Allele Alt Allele
Total Global 14708 C=1.00000 A=0.00000, T=0.00000
European Sub 9768 C=1.0000 A=0.0000, T=0.0000
African Sub 3330 C=1.0000 A=0.0000, T=0.0000
African Others Sub 114 C=1.000 A=0.000, T=0.000
African American Sub 3216 C=1.0000 A=0.0000, T=0.0000
Asian Sub 146 C=1.000 A=0.000, T=0.000
East Asian Sub 120 C=1.000 A=0.000, T=0.000
Other Asian Sub 26 C=1.00 A=0.00, T=0.00
Latin American 1 Sub 146 C=1.000 A=0.000, T=0.000
Latin American 2 Sub 610 C=1.000 A=0.000, T=0.000
South Asian Sub 104 C=1.000 A=0.000, T=0.000
Other Sub 604 C=1.000 A=0.000, T=0.000


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
TopMed Global Study-wide 264690 C=0.999992 T=0.000008
gnomAD - Exomes Global Study-wide 250614 C=0.999996 T=0.000004
gnomAD - Exomes European Sub 134996 C=1.000000 T=0.000000
gnomAD - Exomes Asian Sub 48798 C=1.00000 T=0.00000
gnomAD - Exomes American Sub 34502 C=0.99997 T=0.00003
gnomAD - Exomes African Sub 16134 C=1.00000 T=0.00000
gnomAD - Exomes Ashkenazi Jewish Sub 10056 C=1.00000 T=0.00000
gnomAD - Exomes Other Sub 6128 C=1.0000 T=0.0000
gnomAD - Genomes Global Study-wide 140210 C=0.999993 T=0.000007
gnomAD - Genomes European Sub 75930 C=0.99999 T=0.00001
gnomAD - Genomes African Sub 42020 C=1.00000 T=0.00000
gnomAD - Genomes American Sub 13658 C=1.00000 T=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3322 C=1.0000 T=0.0000
gnomAD - Genomes East Asian Sub 3130 C=1.0000 T=0.0000
gnomAD - Genomes Other Sub 2150 C=1.0000 T=0.0000
The PAGE Study Global Study-wide 78698 C=0.99999 A=0.00001
The PAGE Study AfricanAmerican Sub 32514 C=1.00000 A=0.00000
The PAGE Study Mexican Sub 10808 C=1.00000 A=0.00000
The PAGE Study Asian Sub 8318 C=1.0000 A=0.0000
The PAGE Study PuertoRican Sub 7918 C=0.9999 A=0.0001
The PAGE Study NativeHawaiian Sub 4534 C=1.0000 A=0.0000
The PAGE Study Cuban Sub 4230 C=1.0000 A=0.0000
The PAGE Study Dominican Sub 3828 C=1.0000 A=0.0000
The PAGE Study CentralAmerican Sub 2450 C=1.0000 A=0.0000
The PAGE Study SouthAmerican Sub 1982 C=1.0000 A=0.0000
The PAGE Study NativeAmerican Sub 1260 C=1.0000 A=0.0000
The PAGE Study SouthAsian Sub 856 C=1.000 A=0.000
Allele Frequency Aggregator Total Global 14708 C=1.00000 A=0.00000, T=0.00000
Allele Frequency Aggregator European Sub 9768 C=1.0000 A=0.0000, T=0.0000
Allele Frequency Aggregator African Sub 3330 C=1.0000 A=0.0000, T=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 C=1.000 A=0.000, T=0.000
Allele Frequency Aggregator Other Sub 604 C=1.000 A=0.000, T=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 C=1.000 A=0.000, T=0.000
Allele Frequency Aggregator Asian Sub 146 C=1.000 A=0.000, T=0.000
Allele Frequency Aggregator South Asian Sub 104 C=1.000 A=0.000, T=0.000
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.p14 chr 13 NC_000013.11:g.40793270C>A
GRCh38.p14 chr 13 NC_000013.11:g.40793270C>T
GRCh37.p13 chr 13 NC_000013.10:g.41367406C>A
GRCh37.p13 chr 13 NC_000013.10:g.41367406C>T
SLC25A15 RefSeqGene NG_012248.1:g.8860C>A
SLC25A15 RefSeqGene NG_012248.1:g.8860C>T
Gene: SLC25A15, solute carrier family 25 member 15 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
SLC25A15 transcript NM_014252.4:c.44C>A A [GCG] > E [GAG] Coding Sequence Variant
mitochondrial ornithine transporter 1 NP_055067.1:p.Ala15Glu A (Ala) > E (Glu) Missense Variant
SLC25A15 transcript NM_014252.4:c.44C>T A [GCG] > V [GTG] Coding Sequence Variant
mitochondrial ornithine transporter 1 NP_055067.1:p.Ala15Val A (Ala) > V (Val) 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: T (allele ID: 961871 )
ClinVar Accession Disease Names Clinical Significance
RCV001250167.1 Hyperornithinemia-hyperammonemia-homocitrullinuria syndrome Likely-Pathogenic
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
GRCh38.p14 chr 13 NC_000013.11:g.40793270= NC_000013.11:g.40793270C>A NC_000013.11:g.40793270C>T
GRCh37.p13 chr 13 NC_000013.10:g.41367406= NC_000013.10:g.41367406C>A NC_000013.10:g.41367406C>T
SLC25A15 RefSeqGene NG_012248.1:g.8860= NG_012248.1:g.8860C>A NG_012248.1:g.8860C>T
SLC25A15 transcript NM_014252.4:c.44= NM_014252.4:c.44C>A NM_014252.4:c.44C>T
SLC25A15 transcript NM_014252.3:c.44= NM_014252.3:c.44C>A NM_014252.3:c.44C>T
mitochondrial ornithine transporter 1 NP_055067.1:p.Ala15= NP_055067.1:p.Ala15Glu NP_055067.1:p.Ala15Val
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#.

9 SubSNP, 5 Frequency, 1 ClinVar submissions
No Submitter Submission ID Date (Build)
1 GENEREVIEWS ss531624683 Jun 18, 2012 (136)
2 ILLUMINA ss1959496677 Feb 12, 2016 (147)
3 GNOMAD ss2740381239 Nov 08, 2017 (151)
4 ILLUMINA ss3021502817 Nov 08, 2017 (151)
5 ILLUMINA ss3651888654 Oct 12, 2018 (152)
6 ILLUMINA ss3725389172 Jul 13, 2019 (153)
7 PAGE_CC ss3771742638 Jul 13, 2019 (153)
8 GNOMAD ss4264726515 Apr 26, 2021 (155)
9 TOPMED ss4944013972 Apr 26, 2021 (155)
10 gnomAD - Genomes NC_000013.11 - 40793270 Apr 26, 2021 (155)
11 gnomAD - Exomes NC_000013.10 - 41367406 Jul 13, 2019 (153)
12 The PAGE Study NC_000013.11 - 40793270 Jul 13, 2019 (153)
13 TopMed NC_000013.11 - 40793270 Apr 26, 2021 (155)
14 ALFA NC_000013.11 - 40793270 Apr 26, 2021 (155)
15 ClinVar RCV001250167.1 Apr 26, 2021 (155)
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
ss1959496677, ss3021502817, ss3651888654 NC_000013.10:41367405:C:A NC_000013.11:40793269:C:A (self)
964107, 5199608505, ss531624683, ss3725389172, ss3771742638 NC_000013.11:40793269:C:A NC_000013.11:40793269:C:A (self)
9624845, ss2740381239 NC_000013.10:41367405:C:T NC_000013.11:40793269:C:T (self)
RCV001250167.1, 428854652, 159559630, 5199608505, ss4264726515, ss4944013972 NC_000013.11:40793269:C:T NC_000013.11:40793269: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.

1 citation for rs202247806
PMID Title Author Year Journal
22649802 Hyperornithinemia-Hyperammonemia-Homocitrullinuria Syndrome. Camacho J et al. 1993 GeneReviews(®)
Help

The Flanks tab provides retrieving flanking sequences of a SNP on all molecules that have placements.

Genome context:
Select flank length:

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.post761+d5e8e07