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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.

rs11594082

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr10:71539496 (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>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.103891 (27499/264690, TOPMED)
T=0.106317 (14847/139648, GnomAD)
T=0.08814 (6937/78702, PAGE_STUDY) (+ 14 more)
T=0.10835 (3738/34498, ALFA)
T=0.0770 (493/6404, 1000G_30x)
T=0.0725 (363/5008, 1000G)
T=0.0926 (415/4480, Estonian)
T=0.1173 (452/3854, ALSPAC)
T=0.1146 (425/3708, TWINSUK)
T=0.1252 (195/1558, HapMap)
T=0.087 (87/998, GoNL)
T=0.077 (46/600, NorthernSweden)
T=0.139 (30/216, Qatari)
T=0.014 (3/214, Vietnamese)
G=0.44 (31/70, SGDP_PRJ)
T=0.17 (7/40, GENOME_DK)
G=0.4 (4/10, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
CDH23 : Intron Variant
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: 20230706150541
Population Group Sample Size Ref Allele Alt Allele
Total Global 34498 G=0.89165 T=0.10835
European Sub 21316 G=0.88863 T=0.11137
African Sub 7856 G=0.8768 T=0.1232
African Others Sub 244 G=0.885 T=0.115
African American Sub 7612 G=0.8765 T=0.1235
Asian Sub 206 G=1.000 T=0.000
East Asian Sub 146 G=1.000 T=0.000
Other Asian Sub 60 G=1.00 T=0.00
Latin American 1 Sub 314 G=0.892 T=0.108
Latin American 2 Sub 2826 G=0.9370 T=0.0630
South Asian Sub 116 G=0.991 T=0.009
Other Sub 1864 G=0.9018 T=0.0982


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 G=0.896109 T=0.103891
gnomAD - Genomes Global Study-wide 139648 G=0.893683 T=0.106317
gnomAD - Genomes European Sub 75702 G=0.89328 T=0.10672
gnomAD - Genomes African Sub 41762 G=0.87915 T=0.12085
gnomAD - Genomes American Sub 13594 G=0.91893 T=0.08107
gnomAD - Genomes Ashkenazi Jewish Sub 3320 G=0.8789 T=0.1211
gnomAD - Genomes East Asian Sub 3126 G=0.9997 T=0.0003
gnomAD - Genomes Other Sub 2144 G=0.8993 T=0.1007
The PAGE Study Global Study-wide 78702 G=0.91186 T=0.08814
The PAGE Study AfricanAmerican Sub 32516 G=0.87781 T=0.12219
The PAGE Study Mexican Sub 10810 G=0.93451 T=0.06549
The PAGE Study Asian Sub 8318 G=0.9988 T=0.0012
The PAGE Study PuertoRican Sub 7918 G=0.8954 T=0.1046
The PAGE Study NativeHawaiian Sub 4534 G=0.9720 T=0.0280
The PAGE Study Cuban Sub 4230 G=0.8969 T=0.1031
The PAGE Study Dominican Sub 3828 G=0.8939 T=0.1061
The PAGE Study CentralAmerican Sub 2450 G=0.9327 T=0.0673
The PAGE Study SouthAmerican Sub 1982 G=0.9425 T=0.0575
The PAGE Study NativeAmerican Sub 1260 G=0.8944 T=0.1056
The PAGE Study SouthAsian Sub 856 G=0.957 T=0.043
Allele Frequency Aggregator Total Global 34498 G=0.89165 T=0.10835
Allele Frequency Aggregator European Sub 21316 G=0.88863 T=0.11137
Allele Frequency Aggregator African Sub 7856 G=0.8768 T=0.1232
Allele Frequency Aggregator Latin American 2 Sub 2826 G=0.9370 T=0.0630
Allele Frequency Aggregator Other Sub 1864 G=0.9018 T=0.0982
Allele Frequency Aggregator Latin American 1 Sub 314 G=0.892 T=0.108
Allele Frequency Aggregator Asian Sub 206 G=1.000 T=0.000
Allele Frequency Aggregator South Asian Sub 116 G=0.991 T=0.009
1000Genomes_30x Global Study-wide 6404 G=0.9230 T=0.0770
1000Genomes_30x African Sub 1786 G=0.8701 T=0.1299
1000Genomes_30x Europe Sub 1266 G=0.8926 T=0.1074
1000Genomes_30x South Asian Sub 1202 G=0.9742 T=0.0258
1000Genomes_30x East Asian Sub 1170 G=0.9983 T=0.0017
1000Genomes_30x American Sub 980 G=0.906 T=0.094
1000Genomes Global Study-wide 5008 G=0.9275 T=0.0725
1000Genomes African Sub 1322 G=0.8707 T=0.1293
1000Genomes East Asian Sub 1008 G=0.9980 T=0.0020
1000Genomes Europe Sub 1006 G=0.8956 T=0.1044
1000Genomes South Asian Sub 978 G=0.974 T=0.026
1000Genomes American Sub 694 G=0.914 T=0.086
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.9074 T=0.0926
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.8827 T=0.1173
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.8854 T=0.1146
HapMap Global Study-wide 1558 G=0.8748 T=0.1252
HapMap African Sub 692 G=0.822 T=0.178
HapMap American Sub 600 G=0.913 T=0.087
HapMap Europe Sub 176 G=0.886 T=0.114
HapMap Asian Sub 90 G=1.00 T=0.00
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.913 T=0.087
Northern Sweden ACPOP Study-wide 600 G=0.923 T=0.077
Qatari Global Study-wide 216 G=0.861 T=0.139
A Vietnamese Genetic Variation Database Global Study-wide 214 G=0.986 T=0.014
SGDP_PRJ Global Study-wide 70 G=0.44 T=0.56
The Danish reference pan genome Danish Study-wide 40 G=0.82 T=0.17
Siberian Global Study-wide 10 G=0.4 T=0.6
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 10 NC_000010.11:g.71539496G>T
GRCh37.p13 chr 10 NC_000010.10:g.73299253G>T
CDH23 RefSeqGene NG_008835.1:g.147550G>T
Gene: CDH23, cadherin related 23 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
CDH23 transcript variant 3 NM_001171930.2:c.430-2724…

NM_001171930.2:c.430-27246G>T

 		N/A Intron Variant
CDH23 transcript variant 4 NM_001171931.2:c.430-2724…

NM_001171931.2:c.430-27246G>T

 		N/A Intron Variant
CDH23 transcript variant 5 NM_001171932.2:c.430-2724…

NM_001171932.2:c.430-27246G>T

 		N/A Intron Variant
CDH23 transcript variant 1 NM_022124.6:c.430-27246G>T N/A Intron Variant
CDH23 transcript variant 2 NM_052836.4:c.430-27246G>T N/A Intron Variant
CDH23 transcript variant 6 NM_001171933.1:c. N/A Genic Upstream Transcript Variant
CDH23 transcript variant 7 NM_001171934.1:c. N/A Genic Upstream Transcript Variant
CDH23 transcript variant 8 NM_001171935.1:c. N/A Genic Upstream Transcript Variant
CDH23 transcript variant 9 NM_001171936.1:c. N/A Genic Upstream 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 G= T
GRCh38.p14 chr 10 NC_000010.11:g.71539496= NC_000010.11:g.71539496G>T
GRCh37.p13 chr 10 NC_000010.10:g.73299253= NC_000010.10:g.73299253G>T
CDH23 RefSeqGene NG_008835.1:g.147550= NG_008835.1:g.147550G>T
CDH23 transcript variant 3 NM_001171930.1:c.430-27246= NM_001171930.1:c.430-27246G>T
CDH23 transcript variant 3 NM_001171930.2:c.430-27246= NM_001171930.2:c.430-27246G>T
CDH23 transcript variant 4 NM_001171931.1:c.430-27246= NM_001171931.1:c.430-27246G>T
CDH23 transcript variant 4 NM_001171931.2:c.430-27246= NM_001171931.2:c.430-27246G>T
CDH23 transcript variant 5 NM_001171932.1:c.430-27246= NM_001171932.1:c.430-27246G>T
CDH23 transcript variant 5 NM_001171932.2:c.430-27246= NM_001171932.2:c.430-27246G>T
CDH23 transcript variant 1 NM_022124.5:c.430-27246= NM_022124.5:c.430-27246G>T
CDH23 transcript variant 1 NM_022124.6:c.430-27246= NM_022124.6:c.430-27246G>T
CDH23 transcript variant 2 NM_052836.3:c.430-27246= NM_052836.3:c.430-27246G>T
CDH23 transcript variant 2 NM_052836.4:c.430-27246= NM_052836.4:c.430-27246G>T
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#.

63 SubSNP, 17 Frequency submissions
No Submitter Submission ID Date (Build)
1 CSHL-HAPMAP ss16478608 Feb 28, 2004 (120)
2 PERLEGEN ss23624806 Sep 20, 2004 (123)
3 AFFY ss66191262 Dec 01, 2006 (127)
4 PERLEGEN ss69083420 May 17, 2007 (127)
5 ILLUMINA ss75004904 Dec 06, 2007 (129)
6 AFFY ss76267650 Dec 06, 2007 (129)
7 KRIBB_YJKIM ss82892027 Dec 14, 2007 (130)
8 BCMHGSC_JDW ss88265675 Mar 23, 2008 (129)
9 ENSEMBL ss131946355 Dec 01, 2009 (137)
10 ENSEMBL ss161359299 Dec 01, 2009 (137)
11 ILLUMINA ss171324117 Jul 04, 2010 (137)
12 AFFY ss173043022 Jul 04, 2010 (137)
13 BUSHMAN ss201693083 Jul 04, 2010 (137)
14 BCM-HGSC-SUB ss207321627 Jul 04, 2010 (137)
15 1000GENOMES ss224801555 Jul 14, 2010 (137)
16 1000GENOMES ss235232856 Jul 15, 2010 (137)
17 BL ss254421293 May 09, 2011 (137)
18 ILLUMINA ss536701563 Sep 08, 2015 (146)
19 TISHKOFF ss562043353 Apr 25, 2013 (138)
20 EVA-GONL ss987634249 Aug 21, 2014 (142)
21 JMKIDD_LAB ss1077096403 Aug 21, 2014 (142)
22 1000GENOMES ss1337979689 Aug 21, 2014 (142)
23 DDI ss1426364687 Apr 01, 2015 (144)
24 EVA_GENOME_DK ss1575205245 Apr 01, 2015 (144)
25 EVA_DECODE ss1597306084 Apr 01, 2015 (144)
26 EVA_UK10K_ALSPAC ss1624854490 Apr 01, 2015 (144)
27 EVA_UK10K_TWINSUK ss1667848523 Apr 01, 2015 (144)
28 EVA_SVP ss1713190239 Apr 01, 2015 (144)
29 HAMMER_LAB ss1806452933 Sep 08, 2015 (146)
30 WEILL_CORNELL_DGM ss1930999683 Feb 12, 2016 (147)
31 ILLUMINA ss1959272703 Feb 12, 2016 (147)
32 JJLAB ss2026227544 Sep 14, 2016 (149)
33 USC_VALOUEV ss2154501735 Dec 20, 2016 (150)
34 HUMAN_LONGEVITY ss2175858332 Dec 20, 2016 (150)
35 GNOMAD ss2890295504 Nov 08, 2017 (151)
36 AFFY ss2985560767 Nov 08, 2017 (151)
37 SWEGEN ss3006701627 Nov 08, 2017 (151)
38 ILLUMINA ss3021251392 Nov 08, 2017 (151)
39 BIOINF_KMB_FNS_UNIBA ss3026905520 Nov 08, 2017 (151)
40 CSHL ss3349189766 Nov 08, 2017 (151)
41 ILLUMINA ss3626475393 Oct 12, 2018 (152)
42 ILLUMINA ss3637857554 Oct 12, 2018 (152)
43 ILLUMINA ss3642860507 Oct 12, 2018 (152)
44 ILLUMINA ss3651607555 Oct 12, 2018 (152)
45 EGCUT_WGS ss3674118146 Jul 13, 2019 (153)
46 EVA_DECODE ss3690149828 Jul 13, 2019 (153)
47 ILLUMINA ss3725167423 Jul 13, 2019 (153)
48 ACPOP ss3737445546 Jul 13, 2019 (153)
49 EVA ss3748269342 Jul 13, 2019 (153)
50 PAGE_CC ss3771566029 Jul 13, 2019 (153)
51 KHV_HUMAN_GENOMES ss3813643248 Jul 13, 2019 (153)
52 EVA ss3832197970 Apr 26, 2020 (154)
53 SGDP_PRJ ss3874491019 Apr 26, 2020 (154)
54 EVA ss4017492651 Apr 26, 2021 (155)
55 TOPMED ss4857040807 Apr 26, 2021 (155)
56 1000G_HIGH_COVERAGE ss5284524560 Oct 16, 2022 (156)
57 EVA ss5394307819 Oct 16, 2022 (156)
58 HUGCELL_USP ss5480054925 Oct 16, 2022 (156)
59 1000G_HIGH_COVERAGE ss5578710106 Oct 16, 2022 (156)
60 SANFORD_IMAGENETICS ss5649563330 Oct 16, 2022 (156)
61 EVA ss5824587080 Oct 16, 2022 (156)
62 EVA ss5879446914 Oct 16, 2022 (156)
63 EVA ss5940840386 Oct 16, 2022 (156)
64 1000Genomes NC_000010.10 - 73299253 Oct 12, 2018 (152)
65 1000Genomes_30x NC_000010.11 - 71539496 Oct 16, 2022 (156)
66 The Avon Longitudinal Study of Parents and Children NC_000010.10 - 73299253 Oct 12, 2018 (152)
67 Genetic variation in the Estonian population NC_000010.10 - 73299253 Oct 12, 2018 (152)
68 The Danish reference pan genome NC_000010.10 - 73299253 Apr 26, 2020 (154)
69 gnomAD - Genomes NC_000010.11 - 71539496 Apr 26, 2021 (155)
70 Genome of the Netherlands Release 5 NC_000010.10 - 73299253 Apr 26, 2020 (154)
71 HapMap NC_000010.11 - 71539496 Apr 26, 2020 (154)
72 Northern Sweden NC_000010.10 - 73299253 Jul 13, 2019 (153)
73 The PAGE Study NC_000010.11 - 71539496 Jul 13, 2019 (153)
74 Qatari NC_000010.10 - 73299253 Apr 26, 2020 (154)
75 SGDP_PRJ NC_000010.10 - 73299253 Apr 26, 2020 (154)
76 Siberian NC_000010.10 - 73299253 Apr 26, 2020 (154)
77 TopMed NC_000010.11 - 71539496 Apr 26, 2021 (155)
78 UK 10K study - Twins NC_000010.10 - 73299253 Oct 12, 2018 (152)
79 A Vietnamese Genetic Variation Database NC_000010.10 - 73299253 Jul 13, 2019 (153)
80 ALFA NC_000010.11 - 71539496 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).

Associated ID History Updated (Build)
rs57182485 Feb 27, 2009 (130)
rs76991564 Jan 15, 2013 (137)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss88265675, ss201693083, ss207321627, ss254421293, ss1597306084, ss1713190239, ss3642860507 NC_000010.9:72969258:G:T NC_000010.11:71539495:G:T (self)
50387895, 27970575, 19856394, 2217812, 12474109, 10730411, 13041613, 26507999, 7018089, 27970575, 6213408, ss224801555, ss235232856, ss536701563, ss562043353, ss987634249, ss1077096403, ss1337979689, ss1426364687, ss1575205245, ss1624854490, ss1667848523, ss1806452933, ss1930999683, ss1959272703, ss2026227544, ss2154501735, ss2890295504, ss2985560767, ss3006701627, ss3021251392, ss3349189766, ss3626475393, ss3637857554, ss3651607555, ss3674118146, ss3737445546, ss3748269342, ss3832197970, ss3874491019, ss4017492651, ss5394307819, ss5649563330, ss5824587080, ss5940840386 NC_000010.10:73299252:G:T NC_000010.11:71539495:G:T (self)
66236041, 356081101, 433735, 787498, 72586462, 11857926767, ss2175858332, ss3026905520, ss3690149828, ss3725167423, ss3771566029, ss3813643248, ss4857040807, ss5284524560, ss5480054925, ss5578710106, ss5879446914 NC_000010.11:71539495:G:T NC_000010.11:71539495:G:T (self)
ss16478608 NT_008583.16:21850407:G:T NC_000010.11:71539495:G:T (self)
ss23624806, ss66191262, ss69083420, ss75004904, ss76267650, ss82892027, ss131946355, ss161359299, ss171324117, ss173043022 NT_030059.13:24103716:G:T NC_000010.11:71539495:G:T (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 rs11594082
PMID Title Author Year Journal
19384554 Genome-wide association studies in ADHD. Franke B et al. 2009 Human genetics
20145962 Molecular genetics of attention-deficit/hyperactivity disorder: an overview. Banaschewski T et al. 2010 European child & adolescent psychiatry
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