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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.

rs12014709

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chrX:67718624 (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>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.160781 (42557/264690, TOPMED)
G=0.155122 (15938/102745, GnomAD)
G=0.09915 (4432/44698, ALFA) (+ 11 more)
G=0.1540 (740/4805, 1000G_30x)
G=0.1499 (566/3775, 1000G)
G=0.0766 (284/3708, TWINSUK)
G=0.0672 (194/2889, ALSPAC)
G=0.0960 (200/2084, HGDP_Stanford)
G=0.2477 (385/1554, HapMap)
G=0.176 (19/108, Qatari)
T=0.18 (11/62, SGDP_PRJ)
G=0.09 (4/44, Ancient Sardinia)
G=0.07 (3/40, GENOME_DK)
T=0.2 (1/4, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
AR : Intron Variant
Publications
4 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 44698 T=0.90085 G=0.09915
European Sub 38846 T=0.91788 G=0.08212
African Sub 3064 T=0.6622 G=0.3378
African Others Sub 134 T=0.552 G=0.448
African American Sub 2930 T=0.6672 G=0.3328
Asian Sub 168 T=0.994 G=0.006
East Asian Sub 136 T=1.000 G=0.000
Other Asian Sub 32 T=0.97 G=0.03
Latin American 1 Sub 236 T=0.881 G=0.119
Latin American 2 Sub 1162 T=0.9415 G=0.0585
South Asian Sub 120 T=0.983 G=0.017
Other Sub 1102 T=0.9020 G=0.0980


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 T=0.839219 G=0.160781
gnomAD - Genomes Global Study-wide 102745 T=0.844878 G=0.155122
gnomAD - Genomes European Sub 56656 T=0.92197 G=0.07803
gnomAD - Genomes African Sub 30601 T=0.66289 G=0.33711
gnomAD - Genomes American Sub 9220 T=0.9121 G=0.0879
gnomAD - Genomes Ashkenazi Jewish Sub 2506 T=0.9381 G=0.0619
gnomAD - Genomes East Asian Sub 2218 T=0.9991 G=0.0009
gnomAD - Genomes Other Sub 1544 T=0.8484 G=0.1516
Allele Frequency Aggregator Total Global 44698 T=0.90085 G=0.09915
Allele Frequency Aggregator European Sub 38846 T=0.91788 G=0.08212
Allele Frequency Aggregator African Sub 3064 T=0.6622 G=0.3378
Allele Frequency Aggregator Latin American 2 Sub 1162 T=0.9415 G=0.0585
Allele Frequency Aggregator Other Sub 1102 T=0.9020 G=0.0980
Allele Frequency Aggregator Latin American 1 Sub 236 T=0.881 G=0.119
Allele Frequency Aggregator Asian Sub 168 T=0.994 G=0.006
Allele Frequency Aggregator South Asian Sub 120 T=0.983 G=0.017
1000Genomes_30x Global Study-wide 4805 T=0.8460 G=0.1540
1000Genomes_30x African Sub 1328 T=0.5806 G=0.4194
1000Genomes_30x Europe Sub 961 T=0.906 G=0.094
1000Genomes_30x South Asian Sub 883 T=0.967 G=0.033
1000Genomes_30x East Asian Sub 878 T=1.000 G=0.000
1000Genomes_30x American Sub 755 T=0.915 G=0.085
1000Genomes Global Study-wide 3775 T=0.8501 G=0.1499
1000Genomes African Sub 1003 T=0.5783 G=0.4217
1000Genomes Europe Sub 766 T=0.910 G=0.090
1000Genomes East Asian Sub 764 T=1.000 G=0.000
1000Genomes South Asian Sub 718 T=0.964 G=0.036
1000Genomes American Sub 524 T=0.908 G=0.092
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.9234 G=0.0766
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 2889 T=0.9328 G=0.0672
HGDP-CEPH-db Supplement 1 Global Study-wide 2084 T=0.9040 G=0.0960
HGDP-CEPH-db Supplement 1 Est_Asia Sub 470 T=1.000 G=0.000
HGDP-CEPH-db Supplement 1 Central_South_Asia Sub 414 T=0.947 G=0.053
HGDP-CEPH-db Supplement 1 Middle_Est Sub 350 T=0.871 G=0.129
HGDP-CEPH-db Supplement 1 Europe Sub 320 T=0.916 G=0.084
HGDP-CEPH-db Supplement 1 Africa Sub 242 T=0.599 G=0.401
HGDP-CEPH-db Supplement 1 America Sub 216 T=0.995 G=0.005
HGDP-CEPH-db Supplement 1 Oceania Sub 72 T=0.89 G=0.11
HapMap Global Study-wide 1554 T=0.7523 G=0.2477
HapMap African Sub 690 T=0.570 G=0.430
HapMap American Sub 600 T=0.890 G=0.110
HapMap Europe Sub 176 T=0.875 G=0.125
HapMap Asian Sub 88 T=1.00 G=0.00
Qatari Global Study-wide 108 T=0.824 G=0.176
SGDP_PRJ Global Study-wide 62 T=0.18 G=0.82
Ancient Sardinia genome-wide 1240k capture data generation and analysis Global Study-wide 44 T=0.91 G=0.09
The Danish reference pan genome Danish Study-wide 40 T=0.93 G=0.07
Siberian Global Study-wide 4 T=0.2 G=0.8
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 X NC_000023.11:g.67718624T>G
GRCh37.p13 chr X NC_000023.10:g.66938466T>G
AR RefSeqGene (LRG_1406) NG_009014.2:g.179593T>G
Gene: AR, androgen receptor (plus strand)
Molecule type Change Amino acid[Codon] SO Term
AR transcript variant 1 NM_000044.6:c.2318+1002T>G N/A Intron Variant
AR transcript variant 2 NM_001011645.3:c.722+1002…

NM_001011645.3:c.722+1002T>G

 		N/A Intron Variant
AR transcript variant 3 NM_001348061.1:c. N/A Genic Downstream Transcript Variant
AR transcript variant 4 NM_001348063.1:c. N/A Genic Downstream Transcript Variant
AR transcript variant 5 NM_001348064.1:c. N/A Genic Downstream Transcript 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 T= G
GRCh38.p14 chr X NC_000023.11:g.67718624= NC_000023.11:g.67718624T>G
GRCh37.p13 chr X NC_000023.10:g.66938466= NC_000023.10:g.66938466T>G
AR RefSeqGene (LRG_1406) NG_009014.2:g.179593= NG_009014.2:g.179593T>G
AR transcript variant 1 NM_000044.3:c.2318+1002= NM_000044.3:c.2318+1002T>G
AR transcript variant 1 NM_000044.6:c.2318+1002= NM_000044.6:c.2318+1002T>G
AR transcript variant 2 NM_001011645.2:c.722+1002= NM_001011645.2:c.722+1002T>G
AR transcript variant 2 NM_001011645.3:c.722+1002= NM_001011645.3:c.722+1002T>G
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#.

46 SubSNP, 14 Frequency submissions
No Submitter Submission ID Date (Build)
1 CSHL-HAPMAP ss18051180 Feb 28, 2004 (120)
2 ABI ss43769763 Mar 13, 2006 (126)
3 ILLUMINA ss66796955 Dec 02, 2006 (127)
4 ILLUMINA ss66975519 Dec 02, 2006 (127)
5 ILLUMINA ss67146617 Dec 02, 2006 (127)
6 KRIBB_YJKIM ss85172793 Dec 15, 2007 (130)
7 ENSEMBL ss161801527 Dec 01, 2009 (131)
8 COMPLETE_GENOMICS ss163134780 Jul 04, 2010 (132)
9 ILLUMINA ss244274959 Jul 04, 2010 (132)
10 1000GENOMES ss341529840 May 09, 2011 (134)
11 ILLUMINA ss536746834 Sep 08, 2015 (146)
12 TISHKOFF ss566890002 Apr 25, 2013 (138)
13 SSMP ss662837534 Apr 25, 2013 (138)
14 ILLUMINA ss825373017 Apr 01, 2015 (144)
15 ILLUMINA ss832712551 Aug 21, 2014 (142)
16 ILLUMINA ss833303279 Aug 21, 2014 (142)
17 JMKIDD_LAB ss1082946032 Aug 21, 2014 (142)
18 1000GENOMES ss1554732582 Apr 01, 2015 (144)
19 EVA_GENOME_DK ss1583405730 Apr 01, 2015 (144)
20 EVA_UK10K_ALSPAC ss1640900443 Apr 01, 2015 (144)
21 EVA_UK10K_TWINSUK ss1683894476 Apr 01, 2015 (144)
22 WEILL_CORNELL_DGM ss1939400284 Feb 12, 2016 (147)
23 USC_VALOUEV ss2159083250 Dec 20, 2016 (150)
24 HUMAN_LONGEVITY ss2317829900 Dec 20, 2016 (150)
25 ILLUMINA ss2635202852 Nov 08, 2017 (151)
26 ILLUMINA ss2711183712 Nov 08, 2017 (151)
27 GNOMAD ss2979685398 Nov 08, 2017 (151)
28 SWEGEN ss3020090834 Nov 08, 2017 (151)
29 BIOINF_KMB_FNS_UNIBA ss3029055037 Nov 08, 2017 (151)
30 ILLUMINA ss3630440196 Oct 12, 2018 (152)
31 ILLUMINA ss3638861388 Oct 12, 2018 (152)
32 ILLUMINA ss3639432962 Oct 12, 2018 (152)
33 ILLUMINA ss3639751792 Oct 12, 2018 (152)
34 ILLUMINA ss3643785658 Oct 12, 2018 (152)
35 EVA ss3770237254 Jul 13, 2019 (153)
36 KHV_HUMAN_GENOMES ss3823045485 Jul 13, 2019 (153)
37 EVA ss3836189452 Apr 27, 2020 (154)
38 HGDP ss3847973804 Apr 27, 2020 (154)
39 SGDP_PRJ ss3891566131 Apr 27, 2020 (154)
40 EVA ss3985946153 Apr 27, 2021 (155)
41 TOPMED ss5125531532 Apr 27, 2021 (155)
42 1000G_HIGH_COVERAGE ss5312776335 Oct 17, 2022 (156)
43 HUGCELL_USP ss5504392064 Oct 17, 2022 (156)
44 1000G_HIGH_COVERAGE ss5621177803 Oct 17, 2022 (156)
45 SANFORD_IMAGENETICS ss5665331383 Oct 17, 2022 (156)
46 EVA ss5978364532 Oct 17, 2022 (156)
47 1000Genomes NC_000023.10 - 66938466 Oct 12, 2018 (152)
48 1000Genomes_30x NC_000023.11 - 67718624 Oct 17, 2022 (156)
49 The Avon Longitudinal Study of Parents and Children NC_000023.10 - 66938466 Oct 12, 2018 (152)
50 The Danish reference pan genome NC_000023.10 - 66938466 Apr 27, 2020 (154)
51 gnomAD - Genomes NC_000023.11 - 67718624 Apr 27, 2021 (155)
52 HGDP-CEPH-db Supplement 1 NC_000023.9 - 66855191 Apr 27, 2020 (154)
53 HapMap NC_000023.11 - 67718624 Apr 27, 2020 (154)
54 Ancient Sardinia genome-wide 1240k capture data generation and analysis NC_000023.10 - 66938466 Apr 27, 2021 (155)
55 Qatari NC_000023.10 - 66938466 Apr 27, 2020 (154)
56 SGDP_PRJ NC_000023.10 - 66938466 Apr 27, 2020 (154)
57 Siberian NC_000023.10 - 66938466 Apr 27, 2020 (154)
58 TopMed NC_000023.11 - 67718624 Apr 27, 2021 (155)
59 UK 10K study - Twins NC_000023.10 - 66938466 Oct 12, 2018 (152)
60 ALFA NC_000023.11 - 67718624 Apr 27, 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).

Associated ID History Updated (Build)
rs59662188 May 25, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss3639432962, ss3639751792 NC_000023.8:66721486:T:G NC_000023.11:67718623:T:G (self)
651696, ss163134780, ss244274959, ss825373017, ss2635202852, ss3643785658, ss3847973804 NC_000023.9:66855190:T:G NC_000023.11:67718623:T:G (self)
82704626, 45641296, 9570667, 1172080, 21442206, 43583111, 11599604, 45641296, ss341529840, ss536746834, ss566890002, ss662837534, ss832712551, ss833303279, ss1082946032, ss1554732582, ss1583405730, ss1640900443, ss1683894476, ss1939400284, ss2159083250, ss2711183712, ss2979685398, ss3020090834, ss3630440196, ss3638861388, ss3770237254, ss3836189452, ss3891566131, ss3985946153, ss5665331383, ss5978364532 NC_000023.10:66938465:T:G NC_000023.11:67718623:T:G (self)
108703738, 582675576, 3989899, 689137889, 14297243255, ss2317829900, ss3029055037, ss3823045485, ss5125531532, ss5312776335, ss5504392064, ss5621177803 NC_000023.11:67718623:T:G NC_000023.11:67718623:T:G (self)
ss18051180 NT_011669.14:5256453:T:G NC_000023.11:67718623:T:G (self)
ss43769763, ss66796955, ss66975519, ss67146617, ss85172793, ss161801527 NT_011669.17:5256453:T:G NC_000023.11:67718623:T:G (self)
Help

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

4 citations for rs12014709
PMID Title Author Year Journal
20880698 Polymorphic variation in the androgen receptor gene: association with risk of testicular germ cell cancer and metastatic disease. Västermark Å et al. 2011 European journal of cancer (Oxford, England
23227263 A potential novel spontaneous preterm birth gene, AR, identified by linkage and association analysis of X chromosomal markers. Karjalainen MK et al. 2012 PloS one
24943593 Pathway-based analysis of GWAs data identifies association of sex determination genes with susceptibility to testicular germ cell tumors. Koster R et al. 2014 Human molecular genetics
32850863 Cryptorchidism and Testicular Tumor: Comprehensive Analysis of Common Clinical Features and Search of SNVs in the KIT and AR Genes. Landero-Huerta DA et al. 2020 Frontiers in cell and developmental biology
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