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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.

rs12455984

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr18:13034 (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
G>A
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.33605 (19931/59310, ALFA)
A=0.30794 (5161/16760, 8.3KJPN)
A=0.0004 (4/9240, 14KJPN) (+ 10 more)
A=0.3195 (936/2930, KOREAN)
A=0.406 (306/754, PRJEB37584)
A=0.039 (21/534, MGP)
G=0.500 (151/302, SGDP_PRJ)
A=0.500 (151/302, SGDP_PRJ)
A=0.269 (78/290, HapMap)
A=0.343 (74/216, Qatari)
A=0.340 (72/212, Vietnamese)
G=0.50 (15/30, Siberian)
A=0.50 (15/30, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
LINC02564 : Intron Variant
Publications
0 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: 20230706150541
Population Group Sample Size Ref Allele Alt Allele
Total Global 59310 G=0.66395 A=0.33605
European Sub 54080 G=0.64344 A=0.35656
African Sub 2342 G=0.9953 A=0.0047
African Others Sub 84 G=1.00 A=0.00
African American Sub 2258 G=0.9951 A=0.0049
Asian Sub 152 G=0.849 A=0.151
East Asian Sub 128 G=0.820 A=0.180
Other Asian Sub 24 G=1.00 A=0.00
Latin American 1 Sub 146 G=1.000 A=0.000
Latin American 2 Sub 630 G=0.983 A=0.017
South Asian Sub 94 G=1.00 A=0.00
Other Sub 1866 G=0.6768 A=0.3232


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 59310 G=0.66395 A=0.33605
Allele Frequency Aggregator European Sub 54080 G=0.64344 A=0.35656
Allele Frequency Aggregator African Sub 2342 G=0.9953 A=0.0047
Allele Frequency Aggregator Other Sub 1866 G=0.6768 A=0.3232
Allele Frequency Aggregator Latin American 2 Sub 630 G=0.983 A=0.017
Allele Frequency Aggregator Asian Sub 152 G=0.849 A=0.151
Allele Frequency Aggregator Latin American 1 Sub 146 G=1.000 A=0.000
Allele Frequency Aggregator South Asian Sub 94 G=1.00 A=0.00
8.3KJPN JAPANESE Study-wide 16760 G=0.69206 A=0.30794
14KJPN JAPANESE Study-wide 9240 G=0.9996 A=0.0004
KOREAN population from KRGDB KOREAN Study-wide 2930 G=0.6805 A=0.3195
CNV burdens in cranial meningiomas Global Study-wide 754 G=0.594 A=0.406
CNV burdens in cranial meningiomas CRM Sub 754 G=0.594 A=0.406
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 G=0.961 A=0.039
SGDP_PRJ Global Study-wide 302 G=0.500 A=0.500
HapMap Global Study-wide 290 G=0.731 A=0.269
HapMap African Sub 110 G=0.827 A=0.173
HapMap American Sub 100 G=0.71 A=0.29
HapMap Asian Sub 80 G=0.62 A=0.38
Qatari Global Study-wide 216 G=0.657 A=0.343
A Vietnamese Genetic Variation Database Global Study-wide 212 G=0.660 A=0.340
Siberian Global Study-wide 30 G=0.50 A=0.50
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 18 NC_000018.10:g.13034G>A
GRCh37.p13 chr 18 NC_000018.9:g.13034G>A
Gene: LINC02564, long intergenic non-protein coding RNA 2564 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
LINC02564 transcript variant 1 NR_149137.1:n. N/A Intron Variant
LINC02564 transcript variant 2 NR_149138.1:n. N/A Intron 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.

Not Reported in ClinVar
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 G= A
GRCh38.p14 chr 18 NC_000018.10:g.13034= NC_000018.10:g.13034G>A
GRCh37.p13 chr 18 NC_000018.9:g.13034= NC_000018.9:g.13034G>A
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#.

64 SubSNP, 11 Frequency submissions
No Submitter Submission ID Date (Build)
1 CSHL-HAPMAP ss19382500 Feb 28, 2004 (120)
2 BCMHGSC_JDW ss90682998 Mar 24, 2008 (129)
3 BGI ss103367798 Dec 01, 2009 (131)
4 1000GENOMES ss110009089 Jan 24, 2009 (130)
5 ENSEMBL ss137217446 Dec 01, 2009 (131)
6 ILLUMINA ss160272652 Dec 01, 2009 (131)
7 COMPLETE_GENOMICS ss167621555 Jul 04, 2010 (132)
8 COMPLETE_GENOMICS ss168827153 Jul 04, 2010 (132)
9 BL ss255419469 May 09, 2011 (134)
10 GMI ss282867573 May 04, 2012 (137)
11 ILLUMINA ss410899741 Sep 17, 2011 (135)
12 ILLUMINA ss479744360 May 04, 2012 (137)
13 ILLUMINA ss479750192 May 04, 2012 (137)
14 ILLUMINA ss480307150 Sep 08, 2015 (146)
15 ILLUMINA ss484670481 May 04, 2012 (137)
16 TISHKOFF ss565450743 Apr 25, 2013 (138)
17 ILLUMINA ss782782094 Sep 08, 2015 (146)
18 ILLUMINA ss832034682 Sep 08, 2015 (146)
19 DDI ss1428118136 Apr 01, 2015 (144)
20 EVA_MGP ss1711478390 Apr 01, 2015 (144)
21 ILLUMINA ss1752247548 Sep 08, 2015 (146)
22 HAMMER_LAB ss1808913032 Sep 08, 2015 (146)
23 WEILL_CORNELL_DGM ss1936874167 Feb 12, 2016 (147)
24 ILLUMINA ss1946481138 Feb 12, 2016 (147)
25 ILLUMINA ss1959780081 Feb 12, 2016 (147)
26 GENOMED ss1968448510 Jul 19, 2016 (147)
27 USC_VALOUEV ss2157700851 Dec 20, 2016 (150)
28 SYSTEMSBIOZJU ss2629099597 Nov 08, 2017 (151)
29 ILLUMINA ss2633434928 Nov 08, 2017 (151)
30 GRF ss2702268261 Nov 08, 2017 (151)
31 ILLUMINA ss2710859473 Nov 08, 2017 (151)
32 SWEGEN ss3016019435 Nov 08, 2017 (151)
33 ILLUMINA ss3021815788 Nov 08, 2017 (151)
34 CSHL ss3351875696 Nov 08, 2017 (151)
35 ILLUMINA ss3625719748 Oct 12, 2018 (152)
36 ILLUMINA ss3633151110 Oct 12, 2018 (152)
37 ILLUMINA ss3633859460 Oct 12, 2018 (152)
38 ILLUMINA ss3634692016 Oct 12, 2018 (152)
39 ILLUMINA ss3636380003 Oct 12, 2018 (152)
40 ILLUMINA ss3637298566 Oct 12, 2018 (152)
41 ILLUMINA ss3640399326 Oct 12, 2018 (152)
42 ILLUMINA ss3644698987 Oct 12, 2018 (152)
43 ILLUMINA ss3652234541 Oct 12, 2018 (152)
44 ILLUMINA ss3744154276 Jul 13, 2019 (153)
45 ILLUMINA ss3744992222 Jul 13, 2019 (153)
46 EVA ss3755020235 Jul 13, 2019 (153)
47 ILLUMINA ss3772489814 Jul 13, 2019 (153)
48 PACBIO ss3788286873 Jul 13, 2019 (153)
49 PACBIO ss3793230095 Jul 13, 2019 (153)
50 PACBIO ss3798116295 Jul 13, 2019 (153)
51 EVA ss3835014343 Apr 27, 2020 (154)
52 EVA ss3841120227 Apr 27, 2020 (154)
53 SGDP_PRJ ss3886373163 Apr 27, 2020 (154)
54 KRGDB ss3936171909 Apr 27, 2020 (154)
55 EVA ss3984728083 Apr 26, 2021 (155)
56 EVA ss4017781930 Apr 26, 2021 (155)
57 TOMMO_GENOMICS ss5223805606 Apr 26, 2021 (155)
58 EVA ss5429475032 Oct 16, 2022 (156)
59 SANFORD_IMAGENETICS ss5660679030 Oct 16, 2022 (156)
60 TOMMO_GENOMICS ss5780469899 Oct 16, 2022 (156)
61 EVA ss5827126885 Oct 16, 2022 (156)
62 EVA ss5847811722 Oct 16, 2022 (156)
63 EVA ss5952080594 Oct 16, 2022 (156)
64 EVA ss5980990447 Oct 16, 2022 (156)
65 HapMap NC_000018.10 - 13034 Apr 27, 2020 (154)
66 KOREAN population from KRGDB NC_000018.9 - 13034 Apr 27, 2020 (154)
67 Medical Genome Project healthy controls from Spanish population NC_000018.9 - 13034 Apr 27, 2020 (154)
68 CNV burdens in cranial meningiomas NC_000018.9 - 13034 Apr 26, 2021 (155)
69 Qatari NC_000018.9 - 13034 Apr 27, 2020 (154)
70 SGDP_PRJ NC_000018.9 - 13034 Apr 27, 2020 (154)
71 Siberian NC_000018.9 - 13034 Apr 27, 2020 (154)
72 8.3KJPN NC_000018.9 - 13034 Apr 26, 2021 (155)
73 14KJPN NC_000018.10 - 13034 Oct 16, 2022 (156)
74 A Vietnamese Genetic Variation Database NC_000018.9 - 13034 Jul 13, 2019 (153)
75 ALFA NC_000018.10 - 13034 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
ss90682998, ss110009089, ss167621555, ss168827153, ss255419469, ss282867573, ss479744360 NC_000018.8:3033:G:A NC_000018.10:13033:G:A (self)
43349303, 594150, 277633, 18916089, 38390143, 10217205, 81774913, 8950999, ss479750192, ss480307150, ss484670481, ss565450743, ss782782094, ss832034682, ss1428118136, ss1711478390, ss1752247548, ss1808913032, ss1936874167, ss1946481138, ss1959780081, ss1968448510, ss2157700851, ss2629099597, ss2633434928, ss2702268261, ss2710859473, ss3016019435, ss3021815788, ss3351875696, ss3625719748, ss3633151110, ss3633859460, ss3634692016, ss3636380003, ss3637298566, ss3640399326, ss3644698987, ss3652234541, ss3744154276, ss3744992222, ss3755020235, ss3772489814, ss3788286873, ss3793230095, ss3798116295, ss3835014343, ss3841120227, ss3886373163, ss3936171909, ss3984728083, ss4017781930, ss5223805606, ss5429475032, ss5660679030, ss5827126885, ss5847811722, ss5952080594, ss5980990447 NC_000018.9:13033:G:A NC_000018.10:13033:G:A (self)
1536866, 114307003, 8715583331, ss5780469899 NC_000018.10:13033:G:A NC_000018.10:13033:G:A (self)
ss19382500 NT_010859.13:3033:G:A NC_000018.10:13033:G:A (self)
ss103367798, ss137217446, ss160272652, ss410899741 NT_010859.14:3033:G:A NC_000018.10:13033:G:A (self)
Help

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

No publications for rs12455984

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