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dbSNP Short Genetic Variations

Examples: rs268, BRCA1 and more Advanced search

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.

rs28358572

Current Build 157

Released September 3, 2024

Organism
Homo sapiens
Position
chrMT:1243 (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
T>C
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.0249 (98/3936, ALFA)
C=0.0180 (20/1112, Daghestan)
C=0.006 (3/534, MGP)
Clinical Significance
Reported in ClinVar
Gene : Consequence
None
Publications
2 citations
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: 20231103111315
Population Group Sample Size Ref Allele Alt Allele Ref HMOZ Alt HMOZ HTRZ HWEP
Total Global 3936 T=0.9751 C=0.0249 0.975102 0.024898 0.0 32
European Sub 2230 T=0.9722 C=0.0278 0.972197 0.027803 0.0 32
African Sub 72 T=1.00 C=0.00 1.0 0.0 0.0 N/A
African Others Sub 0 T=0 C=0 0 0 0 N/A
African American Sub 72 T=1.00 C=0.00 1.0 0.0 0.0 N/A
Asian Sub 26 T=1.00 C=0.00 1.0 0.0 0.0 N/A
East Asian Sub 0 T=0 C=0 0 0 0 N/A
Other Asian Sub 26 T=1.00 C=0.00 1.0 0.0 0.0 N/A
Latin American 1 Sub 0 T=0 C=0 0 0 0 N/A
Latin American 2 Sub 0 T=0 C=0 0 0 0 N/A
South Asian Sub 0 T=0 C=0 0 0 0 N/A
Other Sub 1608 T=0.9776 C=0.0224 0.977612 0.022388 0.0 32


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
Allele Frequency Aggregator Total Global 3936 T=0.9751 C=0.0249
Allele Frequency Aggregator European Sub 2230 T=0.9722 C=0.0278
Allele Frequency Aggregator Other Sub 1608 T=0.9776 C=0.0224
Allele Frequency Aggregator African Sub 72 T=1.00 C=0.00
Allele Frequency Aggregator Asian Sub 26 T=1.00 C=0.00
Allele Frequency Aggregator Latin American 1 Sub 0 T=0 C=0
Allele Frequency Aggregator Latin American 2 Sub 0 T=0 C=0
Allele Frequency Aggregator South Asian Sub 0 T=0 C=0
Genome-wide autozygosity in Daghestan Global Study-wide 1112 T=0.9820 C=0.0180
Genome-wide autozygosity in Daghestan Daghestan Sub 628 T=0.990 C=0.010
Genome-wide autozygosity in Daghestan Near_East Sub 142 T=0.972 C=0.028
Genome-wide autozygosity in Daghestan Europe Sub 108 T=0.981 C=0.019
Genome-wide autozygosity in Daghestan Central Asia Sub 100 T=0.94 C=0.06
Genome-wide autozygosity in Daghestan South Asian Sub 98 T=1.00 C=0.00
Genome-wide autozygosity in Daghestan Caucasus Sub 36 T=0.94 C=0.06
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 T=0.994 C=0.006
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.

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: C (allele ID: 51382 )
ClinVar Accession Disease Names Clinical Significance
RCV000035037.5 not specified Benign
RCV000992377.2 not provided Benign
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 T= C
MT NC_012920.1:m.1243= NC_012920.1:m.1243T>C
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#.

27 SubSNP, 3 Frequency, 2 ClinVar submissions
No Submitter Submission ID Date (Build)
1 BROAD ss37044361 May 24, 2005 (125)
2 PERLEGEN ss69268924 May 16, 2007 (127)
3 AFFY ss76713631 Dec 06, 2007 (131)
4 LMM-PCPGM ss244316774 Jun 15, 2010 (136)
5 ILLUMINA ss410884050 Sep 27, 2011 (147)
6 EXOME_CHIP ss491581293 May 04, 2012 (137)
7 ILLUMINA ss780786481 Jul 19, 2016 (147)
8 ILLUMINA ss783467067 Jul 19, 2016 (147)
9 HAMMER_LAB ss1397805350 Oct 12, 2018 (152)
10 EVA_MGP ss1711594546 Jul 19, 2016 (147)
11 ILLUMINA ss1752791132 Jul 19, 2016 (147)
12 ILLUMINA ss1917715357 Jul 19, 2016 (147)
13 ILLUMINA ss1945966291 Jul 19, 2016 (147)
14 ILLUMINA ss1958161094 Jul 19, 2016 (147)
15 ILLUMINA ss2634932496 Oct 12, 2018 (152)
16 AFFY ss2986125483 Oct 12, 2018 (152)
17 SWEGEN ss3020998442 Oct 12, 2018 (152)
18 ILLUMINA ss3022981151 Oct 12, 2018 (152)
19 ILLUMINA ss3640947696 Oct 12, 2018 (152)
20 ILLUMINA ss3645007053 Oct 12, 2018 (152)
21 ILLUMINA ss3653538683 Oct 12, 2018 (152)
22 ILLUMINA ss3726655972 Jul 14, 2019 (153)
23 ILLUMINA ss3745540276 Jul 14, 2019 (153)
24 ILLUMINA ss3773031996 Jul 14, 2019 (153)
25 SANFORD_IMAGENETICS ss8666159798 Oct 30, 2024 (157)
26 EVA ss8799405163 Oct 30, 2024 (157)
27 EVA ss8848225704 Oct 30, 2024 (157)
28 Genome-wide autozygosity in Daghestan NC_001807.4 - 1245 Apr 27, 2020 (154)
29 Medical Genome Project healthy controls from Spanish population NC_012920.1 - 1243 Apr 27, 2020 (154)
30 ALFA NC_012920.1 - 1243 Oct 30, 2024 (157)
31 ClinVar RCV000035037.5 Oct 30, 2024 (157)
32 ClinVar RCV000992377.2 Oct 30, 2024 (157)
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).

Associated ID History Updated (Build)
rs55647256 Dec 02, 2009 (131)
rs111033172 Mar 28, 2012 (136)
rs193302951 Feb 12, 2016 (147)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
542920, ss76713631, ss1397805350 NC_001807.4:1244:T:C NC_012920.1:1242:T:C (self)
RCV000035037.5, RCV000992377.2, 710306, 6959766484, ss37044361, ss69268924, ss244316774, ss410884050, ss491581293, ss780786481, ss783467067, ss1711594546, ss1752791132, ss1917715357, ss1945966291, ss1958161094, ss2634932496, ss2986125483, ss3020998442, ss3022981151, ss3640947696, ss3645007053, ss3653538683, ss3726655972, ss3745540276, ss3773031996, ss8666159798, ss8799405163, ss8848225704 NC_012920.1:1242:T:C NC_012920.1:1242:T:C (self)
Help

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

2 citations for rs28358572
PMID Title Author Year Journal
11245424 Detection of mitochondrial DNA mutations in pancreatic cancer offers a "mass"-ive advantage over detection of nuclear DNA mutations. Jones JB et al. 2001 Cancer research
24033266 A systematic approach to assessing the clinical significance of genetic variants. Duzkale H et al. 2013 Clinical genetics
Help

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

No flank sequence available

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.post825+45319f0