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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.

rs11206252

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr1:53931567 (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=0.080241 (21239/264690, TOPMED)
A=0.079617 (11157/140134, GnomAD)
A=0.04746 (1341/28258, 14KJPN) (+ 19 more)
A=0.05761 (1346/23362, ALFA)
A=0.05012 (840/16760, 8.3KJPN)
A=0.0864 (553/6404, 1000G_30x)
A=0.0833 (417/5008, 1000G)
A=0.0263 (118/4480, Estonian)
A=0.0368 (142/3854, ALSPAC)
A=0.0270 (100/3708, TWINSUK)
A=0.0459 (134/2922, KOREAN)
A=0.1194 (225/1884, HapMap)
A=0.0469 (86/1832, Korea1K)
A=0.0467 (53/1134, Daghestan)
A=0.031 (31/998, GoNL)
A=0.022 (14/626, Chileans)
A=0.060 (36/600, NorthernSweden)
A=0.074 (16/216, Qatari)
A=0.057 (12/212, Vietnamese)
G=0.47 (32/68, SGDP_PRJ)
G=0.5 (2/4, Siberian)
A=0.5 (2/4, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
HSPB11 : 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 23362 G=0.94239 A=0.05761
European Sub 17382 G=0.96859 A=0.03141
African Sub 3620 G=0.8088 A=0.1912
African Others Sub 126 G=0.738 A=0.262
African American Sub 3494 G=0.8114 A=0.1886
Asian Sub 160 G=0.931 A=0.069
East Asian Sub 102 G=0.951 A=0.049
Other Asian Sub 58 G=0.90 A=0.10
Latin American 1 Sub 212 G=0.920 A=0.080
Latin American 2 Sub 754 G=0.981 A=0.019
South Asian Sub 110 G=0.945 A=0.055
Other Sub 1124 G=0.9466 A=0.0534


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=0.919759 A=0.080241
gnomAD - Genomes Global Study-wide 140134 G=0.920383 A=0.079617
gnomAD - Genomes European Sub 75914 G=0.96731 A=0.03269
gnomAD - Genomes African Sub 41962 G=0.81448 A=0.18552
gnomAD - Genomes American Sub 13650 G=0.96901 A=0.03099
gnomAD - Genomes Ashkenazi Jewish Sub 3320 G=0.9596 A=0.0404
gnomAD - Genomes East Asian Sub 3134 G=0.9387 A=0.0613
gnomAD - Genomes Other Sub 2154 G=0.9345 A=0.0655
14KJPN JAPANESE Study-wide 28258 G=0.95254 A=0.04746
Allele Frequency Aggregator Total Global 23362 G=0.94239 A=0.05761
Allele Frequency Aggregator European Sub 17382 G=0.96859 A=0.03141
Allele Frequency Aggregator African Sub 3620 G=0.8088 A=0.1912
Allele Frequency Aggregator Other Sub 1124 G=0.9466 A=0.0534
Allele Frequency Aggregator Latin American 2 Sub 754 G=0.981 A=0.019
Allele Frequency Aggregator Latin American 1 Sub 212 G=0.920 A=0.080
Allele Frequency Aggregator Asian Sub 160 G=0.931 A=0.069
Allele Frequency Aggregator South Asian Sub 110 G=0.945 A=0.055
8.3KJPN JAPANESE Study-wide 16760 G=0.94988 A=0.05012
1000Genomes_30x Global Study-wide 6404 G=0.9136 A=0.0864
1000Genomes_30x African Sub 1786 G=0.7682 A=0.2318
1000Genomes_30x Europe Sub 1266 G=0.9787 A=0.0213
1000Genomes_30x South Asian Sub 1202 G=0.9759 A=0.0241
1000Genomes_30x East Asian Sub 1170 G=0.9393 A=0.0607
1000Genomes_30x American Sub 980 G=0.988 A=0.012
1000Genomes Global Study-wide 5008 G=0.9167 A=0.0833
1000Genomes African Sub 1322 G=0.7693 A=0.2307
1000Genomes East Asian Sub 1008 G=0.9435 A=0.0565
1000Genomes Europe Sub 1006 G=0.9791 A=0.0209
1000Genomes South Asian Sub 978 G=0.973 A=0.027
1000Genomes American Sub 694 G=0.988 A=0.012
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.9737 A=0.0263
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.9632 A=0.0368
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.9730 A=0.0270
KOREAN population from KRGDB KOREAN Study-wide 2922 G=0.9541 A=0.0459
HapMap Global Study-wide 1884 G=0.8806 A=0.1194
HapMap American Sub 762 G=0.958 A=0.042
HapMap African Sub 692 G=0.757 A=0.243
HapMap Asian Sub 254 G=0.929 A=0.071
HapMap Europe Sub 176 G=0.960 A=0.040
Korean Genome Project KOREAN Study-wide 1832 G=0.9531 A=0.0469
Genome-wide autozygosity in Daghestan Global Study-wide 1134 G=0.9533 A=0.0467
Genome-wide autozygosity in Daghestan Daghestan Sub 628 G=0.955 A=0.045
Genome-wide autozygosity in Daghestan Near_East Sub 144 G=0.903 A=0.097
Genome-wide autozygosity in Daghestan Central Asia Sub 122 G=0.951 A=0.049
Genome-wide autozygosity in Daghestan Europe Sub 108 G=0.981 A=0.019
Genome-wide autozygosity in Daghestan South Asian Sub 98 G=0.98 A=0.02
Genome-wide autozygosity in Daghestan Caucasus Sub 34 G=0.97 A=0.03
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.969 A=0.031
Chileans Chilean Study-wide 626 G=0.978 A=0.022
Northern Sweden ACPOP Study-wide 600 G=0.940 A=0.060
Qatari Global Study-wide 216 G=0.926 A=0.074
A Vietnamese Genetic Variation Database Global Study-wide 212 G=0.943 A=0.057
SGDP_PRJ Global Study-wide 68 G=0.47 A=0.53
Siberian Global Study-wide 4 G=0.5 A=0.5
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 1 NC_000001.11:g.53931567G>A
GRCh37.p13 chr 1 NC_000001.10:g.54397240G>A
Gene: HSPB11, heat shock protein family B (small) member 11 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
IFT25 transcript variant 2 NM_001316935.2:c.99-1422C…

NM_001316935.2:c.99-1422C>T

N/A Intron Variant
IFT25 transcript variant 5 NM_001382249.1:c.99-1422C…

NM_001382249.1:c.99-1422C>T

N/A Intron Variant
IFT25 transcript variant 6 NM_001382250.1:c.99-1422C…

NM_001382250.1:c.99-1422C>T

N/A Intron Variant
IFT25 transcript variant 7 NM_001382251.1:c.-31-1422…

NM_001382251.1:c.-31-1422C>T

N/A Intron Variant
IFT25 transcript variant 8 NM_001382252.1:c.-31-1422…

NM_001382252.1:c.-31-1422C>T

N/A Intron Variant
IFT25 transcript variant 9 NM_001382253.1:c.99-1422C…

NM_001382253.1:c.99-1422C>T

N/A Intron Variant
IFT25 transcript variant 10 NM_001382254.1:c.-31-1422…

NM_001382254.1:c.-31-1422C>T

N/A Intron Variant
IFT25 transcript variant 18 NM_001382261.1:c.99-1422C…

NM_001382261.1:c.99-1422C>T

N/A Intron Variant
IFT25 transcript variant 1 NM_016126.4:c.99-1422C>T N/A Intron Variant
IFT25 transcript variant 3 NR_133632.2:n. N/A Intron Variant
IFT25 transcript variant 4 NR_133633.2:n. N/A Intron Variant
IFT25 transcript variant 11 NR_167989.1:n. N/A Intron Variant
IFT25 transcript variant 12 NR_167990.1:n. N/A Intron Variant
IFT25 transcript variant 13 NR_167991.1:n. N/A Intron Variant
IFT25 transcript variant 14 NR_167992.1:n. N/A Intron Variant
IFT25 transcript variant 15 NR_167993.1:n. N/A Intron Variant
IFT25 transcript variant 16 NR_167994.1:n. N/A Intron Variant
IFT25 transcript variant 17 NR_167995.1:n. N/A Intron Variant
IFT25 transcript variant X1 XM_047422519.1:c.99-1422C…

XM_047422519.1:c.99-1422C>T

N/A Intron Variant
IFT25 transcript variant X2 XM_047422520.1:c.99-1422C…

XM_047422520.1:c.99-1422C>T

N/A Intron Variant
IFT25 transcript variant X3 XM_047422521.1:c.99-1422C…

XM_047422521.1:c.99-1422C>T

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 1 NC_000001.11:g.53931567= NC_000001.11:g.53931567G>A
GRCh37.p13 chr 1 NC_000001.10:g.54397240= NC_000001.10:g.54397240G>A
IFT25 transcript variant 2 NM_001316935.2:c.99-1422= NM_001316935.2:c.99-1422C>T
IFT25 transcript variant 5 NM_001382249.1:c.99-1422= NM_001382249.1:c.99-1422C>T
IFT25 transcript variant 6 NM_001382250.1:c.99-1422= NM_001382250.1:c.99-1422C>T
IFT25 transcript variant 7 NM_001382251.1:c.-31-1422= NM_001382251.1:c.-31-1422C>T
IFT25 transcript variant 8 NM_001382252.1:c.-31-1422= NM_001382252.1:c.-31-1422C>T
IFT25 transcript variant 9 NM_001382253.1:c.99-1422= NM_001382253.1:c.99-1422C>T
IFT25 transcript variant 10 NM_001382254.1:c.-31-1422= NM_001382254.1:c.-31-1422C>T
IFT25 transcript variant 18 NM_001382261.1:c.99-1422= NM_001382261.1:c.99-1422C>T
HSPB11 transcript NM_016126.2:c.99-1422= NM_016126.2:c.99-1422C>T
IFT25 transcript variant 1 NM_016126.4:c.99-1422= NM_016126.4:c.99-1422C>T
HSPB11 transcript variant X1 XM_005270942.1:c.99-1422= XM_005270942.1:c.99-1422C>T
HSPB11 transcript variant X2 XM_005270943.1:c.99-1422= XM_005270943.1:c.99-1422C>T
IFT25 transcript variant X1 XM_047422519.1:c.99-1422= XM_047422519.1:c.99-1422C>T
IFT25 transcript variant X2 XM_047422520.1:c.99-1422= XM_047422520.1:c.99-1422C>T
IFT25 transcript variant X3 XM_047422521.1:c.99-1422= XM_047422521.1:c.99-1422C>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#.

54 SubSNP, 21 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_SNP ss18115490 Feb 27, 2004 (120)
2 SC_SNP ss18202119 Feb 27, 2004 (120)
3 AFFY ss66477039 Nov 29, 2006 (127)
4 AFFY ss76289505 Dec 08, 2007 (130)
5 KRIBB_YJKIM ss82874096 Dec 14, 2007 (130)
6 1000GENOMES ss110444940 Jan 24, 2009 (130)
7 ILLUMINA-UK ss118691574 Feb 14, 2009 (130)
8 COMPLETE_GENOMICS ss163385824 Jul 04, 2010 (132)
9 COMPLETE_GENOMICS ss166511890 Jul 04, 2010 (132)
10 AFFY ss173139538 Jul 04, 2010 (132)
11 BUSHMAN ss198446870 Jul 04, 2010 (132)
12 1000GENOMES ss218380544 Jul 14, 2010 (132)
13 TISHKOFF ss554103943 Apr 25, 2013 (138)
14 SSMP ss647929460 Apr 25, 2013 (138)
15 EVA-GONL ss975152023 Aug 21, 2014 (142)
16 JMKIDD_LAB ss1067879847 Aug 21, 2014 (142)
17 1000GENOMES ss1290862106 Aug 21, 2014 (142)
18 HAMMER_LAB ss1397245166 Sep 08, 2015 (146)
19 DDI ss1425805646 Apr 01, 2015 (144)
20 EVA_DECODE ss1584518082 Apr 01, 2015 (144)
21 EVA_UK10K_ALSPAC ss1600157135 Apr 01, 2015 (144)
22 EVA_UK10K_TWINSUK ss1643151168 Apr 01, 2015 (144)
23 EVA_SVP ss1712332170 Apr 01, 2015 (144)
24 HAMMER_LAB ss1794347383 Sep 08, 2015 (146)
25 WEILL_CORNELL_DGM ss1918360850 Feb 12, 2016 (147)
26 JJLAB ss2019695462 Sep 14, 2016 (149)
27 USC_VALOUEV ss2147709509 Dec 20, 2016 (150)
28 HUMAN_LONGEVITY ss2162442570 Dec 20, 2016 (150)
29 SYSTEMSBIOZJU ss2624360349 Nov 08, 2017 (151)
30 GRF ss2697621270 Nov 08, 2017 (151)
31 GNOMAD ss2755067982 Nov 08, 2017 (151)
32 SWEGEN ss2986804575 Nov 08, 2017 (151)
33 EGCUT_WGS ss3654868190 Jul 12, 2019 (153)
34 EVA_DECODE ss3686755952 Jul 12, 2019 (153)
35 ACPOP ss3727039811 Jul 12, 2019 (153)
36 EVA ss3746193478 Jul 12, 2019 (153)
37 KHV_HUMAN_GENOMES ss3799203002 Jul 12, 2019 (153)
38 EVA ss3826167146 Apr 25, 2020 (154)
39 SGDP_PRJ ss3848830035 Apr 25, 2020 (154)
40 KRGDB ss3893838275 Apr 25, 2020 (154)
41 KOGIC ss3944495135 Apr 25, 2020 (154)
42 TOPMED ss4449488594 Apr 25, 2021 (155)
43 TOMMO_GENOMICS ss5143915811 Apr 25, 2021 (155)
44 1000G_HIGH_COVERAGE ss5242242671 Oct 12, 2022 (156)
45 EVA ss5318675547 Oct 12, 2022 (156)
46 HUGCELL_USP ss5443306824 Oct 12, 2022 (156)
47 EVA ss5505847744 Oct 12, 2022 (156)
48 1000G_HIGH_COVERAGE ss5514506528 Oct 12, 2022 (156)
49 SANFORD_IMAGENETICS ss5625513451 Oct 12, 2022 (156)
50 TOMMO_GENOMICS ss5668678858 Oct 12, 2022 (156)
51 YY_MCH ss5800588501 Oct 12, 2022 (156)
52 EVA ss5831948301 Oct 12, 2022 (156)
53 EVA ss5908228537 Oct 12, 2022 (156)
54 EVA ss5937344510 Oct 12, 2022 (156)
55 1000Genomes NC_000001.10 - 54397240 Oct 11, 2018 (152)
56 1000Genomes_30x NC_000001.11 - 53931567 Oct 12, 2022 (156)
57 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 54397240 Oct 11, 2018 (152)
58 Chileans NC_000001.10 - 54397240 Apr 25, 2020 (154)
59 Genome-wide autozygosity in Daghestan NC_000001.9 - 54169828 Apr 25, 2020 (154)
60 Genetic variation in the Estonian population NC_000001.10 - 54397240 Oct 11, 2018 (152)
61 gnomAD - Genomes NC_000001.11 - 53931567 Apr 25, 2021 (155)
62 Genome of the Netherlands Release 5 NC_000001.10 - 54397240 Apr 25, 2020 (154)
63 HapMap NC_000001.11 - 53931567 Apr 25, 2020 (154)
64 KOREAN population from KRGDB NC_000001.10 - 54397240 Apr 25, 2020 (154)
65 Korean Genome Project NC_000001.11 - 53931567 Apr 25, 2020 (154)
66 Northern Sweden NC_000001.10 - 54397240 Jul 12, 2019 (153)
67 Qatari NC_000001.10 - 54397240 Apr 25, 2020 (154)
68 SGDP_PRJ NC_000001.10 - 54397240 Apr 25, 2020 (154)
69 Siberian NC_000001.10 - 54397240 Apr 25, 2020 (154)
70 8.3KJPN NC_000001.10 - 54397240 Apr 25, 2021 (155)
71 14KJPN NC_000001.11 - 53931567 Oct 12, 2022 (156)
72 TopMed NC_000001.11 - 53931567 Apr 25, 2021 (155)
73 UK 10K study - Twins NC_000001.10 - 54397240 Oct 11, 2018 (152)
74 A Vietnamese Genetic Variation Database NC_000001.10 - 54397240 Jul 12, 2019 (153)
75 ALFA NC_000001.11 - 53931567 Apr 25, 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)
rs56474475 May 26, 2008 (130)
rs57067700 Feb 27, 2009 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
6598, ss66477039, ss76289505, ss110444940, ss118691574, ss163385824, ss166511890, ss173139538, ss198446870, ss1397245166, ss1584518082, ss1712332170 NC_000001.9:54169827:G:A NC_000001.11:53931566:G:A (self)
1579367, 858445, 8041, 606438, 363748, 1015669, 324676, 402780, 847015, 225863, 1885118, 858445, 175752, ss218380544, ss554103943, ss647929460, ss975152023, ss1067879847, ss1290862106, ss1425805646, ss1600157135, ss1643151168, ss1794347383, ss1918360850, ss2019695462, ss2147709509, ss2624360349, ss2697621270, ss2755067982, ss2986804575, ss3654868190, ss3727039811, ss3746193478, ss3826167146, ss3848830035, ss3893838275, ss5143915811, ss5318675547, ss5505847744, ss5625513451, ss5831948301, ss5937344510 NC_000001.10:54397239:G:A NC_000001.11:53931566:G:A (self)
2032463, 11187412, 66635, 873136, 2515962, 13094929, 642340542, ss2162442570, ss3686755952, ss3799203002, ss3944495135, ss4449488594, ss5242242671, ss5443306824, ss5514506528, ss5668678858, ss5800588501, ss5908228537 NC_000001.11:53931566:G:A NC_000001.11:53931566:G:A (self)
ss18115490, ss18202119 NT_032977.6:15960310:G:A NC_000001.11:53931566:G:A (self)
ss82874096 NT_032977.9:24369157:G:A NC_000001.11:53931566: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 rs11206252

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