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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.

rs709766

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:85095863 (GRCh38.p13) 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
T=0.402191 (106456/264690, TOPMED)
T=0.408536 (57164/139924, GnomAD)
T=0.42614 (19299/45288, ALFA) (+ 16 more)
C=0.45107 (7560/16760, 8.3KJPN)
T=0.4301 (2154/5008, 1000G)
C=0.4942 (2214/4480, Estonian)
T=0.4237 (1633/3854, ALSPAC)
T=0.4345 (1611/3708, TWINSUK)
C=0.4512 (1322/2930, KOREAN)
T=0.4335 (815/1880, HapMap)
C=0.4814 (882/1832, Korea1K)
T=0.440 (439/998, GoNL)
T=0.467 (280/600, NorthernSweden)
T=0.440 (235/534, MGP)
T=0.340 (147/432, SGDP_PRJ)
T=0.431 (93/216, Qatari)
C=0.477 (102/214, Vietnamese)
T=0.32 (16/50, Siberian)
T=0.40 (16/40, GENOME_DK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
DNAI3 : Intron Variant
Publications
0 citations
Genomic View
See rs on genome
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.p13 chr 1 NC_000001.11:g.85095863T>C
GRCh37.p13 chr 1 NC_000001.10:g.85561546T>C
Gene: DNAI3, dynein axonemal intermediate chain 3 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
DNAI3 transcript variant 2 NM_001288563.2:c.1057-68T…

NM_001288563.2:c.1057-68T>C

N/A Intron Variant
DNAI3 transcript variant 1 NM_145172.5:c.1174-68T>C 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

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: 20201027095038
Population Group Sample Size Ref Allele Alt Allele
Total Global 45288 T=0.42614 C=0.57386
European Sub 33910 T=0.44432 C=0.55568
African Sub 5002 T=0.3437 C=0.6563
African Others Sub 170 T=0.312 C=0.688
African American Sub 4832 T=0.3448 C=0.6552
Asian Sub 184 T=0.554 C=0.446
East Asian Sub 124 T=0.565 C=0.435
Other Asian Sub 60 T=0.53 C=0.47
Latin American 1 Sub 328 T=0.384 C=0.616
Latin American 2 Sub 2912 T=0.3688 C=0.6312
South Asian Sub 126 T=0.460 C=0.540
Other Sub 2826 T=0.4080 C=0.5920


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=0.402191 C=0.597809
gnomAD - Genomes Global Study-wide 139924 T=0.408536 C=0.591464
gnomAD - Genomes European Sub 75804 T=0.44002 C=0.55998
gnomAD - Genomes African Sub 41908 T=0.33476 C=0.66524
gnomAD - Genomes American Sub 13628 T=0.39632 C=0.60368
gnomAD - Genomes Ashkenazi Jewish Sub 3316 T=0.5148 C=0.4852
gnomAD - Genomes East Asian Sub 3124 T=0.5810 C=0.4190
gnomAD - Genomes Other Sub 2144 T=0.3997 C=0.6003
8.3KJPN JAPANESE Study-wide 16760 T=0.54893 C=0.45107
1000Genomes Global Study-wide 5008 T=0.4301 C=0.5699
1000Genomes African Sub 1322 T=0.3298 C=0.6702
1000Genomes East Asian Sub 1008 T=0.5625 C=0.4375
1000Genomes Europe Sub 1006 T=0.4284 C=0.5716
1000Genomes South Asian Sub 978 T=0.471 C=0.529
1000Genomes American Sub 694 T=0.373 C=0.627
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.5058 C=0.4942
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.4237 C=0.5763
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.4345 C=0.5655
KOREAN population from KRGDB KOREAN Study-wide 2930 T=0.5488 C=0.4512
HapMap Global Study-wide 1880 T=0.4335 C=0.5665
HapMap American Sub 760 T=0.453 C=0.547
HapMap African Sub 692 T=0.348 C=0.652
HapMap Asian Sub 252 T=0.603 C=0.397
HapMap Europe Sub 176 T=0.443 C=0.557
Korean Genome Project KOREAN Study-wide 1832 T=0.5186 C=0.4814
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 T=0.440 C=0.560
Northern Sweden ACPOP Study-wide 600 T=0.467 C=0.533
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 T=0.440 C=0.560
SGDP_PRJ Global Study-wide 432 T=0.340 C=0.660
Qatari Global Study-wide 216 T=0.431 C=0.569
A Vietnamese Genetic Variation Database Global Study-wide 214 T=0.523 C=0.477
Siberian Global Study-wide 50 T=0.32 C=0.68
The Danish reference pan genome Danish Study-wide 40 T=0.40 C=0.60
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
GRCh38.p13 chr 1 NC_000001.11:g.85095863= NC_000001.11:g.85095863T>C
GRCh37.p13 chr 1 NC_000001.10:g.85561546= NC_000001.10:g.85561546T>C
DNAI3 transcript variant 2 NM_001288563.2:c.1057-68= NM_001288563.2:c.1057-68T>C
WDR63 transcript NM_145172.3:c.1174-68= NM_145172.3:c.1174-68T>C
DNAI3 transcript variant 1 NM_145172.5:c.1174-68= NM_145172.5:c.1174-68T>C
WDR63 transcript variant X1 XM_005270437.1:c.1057-68= XM_005270437.1:c.1057-68T>C
WDR63 transcript variant X2 XM_005270438.1:c.1174-68= XM_005270438.1:c.1174-68T>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#.

101 SubSNP, 19 Frequency submissions
No Submitter Submission ID Date (Build)
1 KWOK ss1080875 Oct 04, 2000 (86)
2 KWOK ss1081286 Oct 04, 2000 (86)
3 KWOK ss1883472 Oct 18, 2000 (87)
4 KWOK ss1884009 Oct 18, 2000 (87)
5 SC_JCM ss2629882 Nov 08, 2000 (89)
6 WI_SSAHASNP ss11350791 Jul 11, 2003 (116)
7 SC_SNP ss15423874 Feb 27, 2004 (120)
8 ABI ss44123851 Mar 13, 2006 (126)
9 ILLUMINA ss65761479 Oct 13, 2006 (127)
10 SI_EXO ss71644655 May 16, 2007 (127)
11 ILLUMINA ss74855135 Dec 07, 2007 (129)
12 AFFY ss76855480 Dec 07, 2007 (129)
13 HGSV ss78399243 Dec 07, 2007 (129)
14 HGSV ss79016393 Dec 07, 2007 (129)
15 BCMHGSC_JDW ss87594130 Mar 23, 2008 (129)
16 HUMANGENOME_JCVI ss99224850 Feb 04, 2009 (130)
17 BGI ss102759384 Dec 01, 2009 (131)
18 1000GENOMES ss108376197 Jan 23, 2009 (130)
19 1000GENOMES ss110753309 Jan 25, 2009 (130)
20 ILLUMINA-UK ss118858900 Feb 14, 2009 (130)
21 KRIBB_YJKIM ss119363918 Dec 01, 2009 (131)
22 ENSEMBL ss138027948 Dec 01, 2009 (131)
23 ENSEMBL ss138874066 Dec 01, 2009 (131)
24 COMPLETE_GENOMICS ss163602552 Jul 04, 2010 (132)
25 COMPLETE_GENOMICS ss164691312 Jul 04, 2010 (132)
26 COMPLETE_GENOMICS ss166785762 Jul 04, 2010 (132)
27 ILLUMINA ss174239405 Jul 04, 2010 (132)
28 BUSHMAN ss198716033 Jul 04, 2010 (132)
29 BCM-HGSC-SUB ss205332568 Jul 04, 2010 (132)
30 1000GENOMES ss218498677 Jul 14, 2010 (132)
31 1000GENOMES ss230618179 Jul 14, 2010 (132)
32 1000GENOMES ss238294624 Jul 15, 2010 (132)
33 BL ss253243983 May 09, 2011 (134)
34 GMI ss275908380 May 04, 2012 (137)
35 GMI ss284088087 Apr 25, 2013 (138)
36 PJP ss290553632 May 09, 2011 (134)
37 ILLUMINA ss482420040 May 04, 2012 (137)
38 ILLUMINA ss483099687 May 04, 2012 (137)
39 ILLUMINA ss535280994 Sep 08, 2015 (146)
40 TISHKOFF ss554376172 Apr 25, 2013 (138)
41 SSMP ss648186324 Apr 25, 2013 (138)
42 ILLUMINA ss780150831 Aug 21, 2014 (142)
43 ILLUMINA ss781993190 Aug 21, 2014 (142)
44 ILLUMINA ss835634416 Aug 21, 2014 (142)
45 EVA-GONL ss975380208 Aug 21, 2014 (142)
46 JMKIDD_LAB ss1068053449 Aug 21, 2014 (142)
47 1000GENOMES ss1291721612 Aug 21, 2014 (142)
48 DDI ss1425881203 Apr 01, 2015 (144)
49 EVA_GENOME_DK ss1574200498 Apr 01, 2015 (144)
50 EVA_DECODE ss1584754240 Apr 01, 2015 (144)
51 EVA_UK10K_ALSPAC ss1600609145 Apr 01, 2015 (144)
52 EVA_UK10K_TWINSUK ss1643603178 Apr 01, 2015 (144)
53 EVA_MGP ss1710910702 Apr 01, 2015 (144)
54 EVA_SVP ss1712349517 Apr 01, 2015 (144)
55 HAMMER_LAB ss1794671632 Sep 08, 2015 (146)
56 WEILL_CORNELL_DGM ss1918582995 Feb 12, 2016 (147)
57 GENOMED ss1966797306 Jul 19, 2016 (147)
58 JJLAB ss2019812025 Sep 14, 2016 (149)
59 USC_VALOUEV ss2147828823 Dec 20, 2016 (150)
60 HUMAN_LONGEVITY ss2164223489 Dec 20, 2016 (150)
61 TOPMED ss2326537048 Dec 20, 2016 (150)
62 SYSTEMSBIOZJU ss2624417151 Nov 08, 2017 (151)
63 ILLUMINA ss2632541531 Nov 08, 2017 (151)
64 GRF ss2697752181 Nov 08, 2017 (151)
65 GNOMAD ss2757515083 Nov 08, 2017 (151)
66 AFFY ss2984866012 Nov 08, 2017 (151)
67 AFFY ss2985518380 Nov 08, 2017 (151)
68 SWEGEN ss2987147714 Nov 08, 2017 (151)
69 BIOINF_KMB_FNS_UNIBA ss3023668737 Nov 08, 2017 (151)
70 TOPMED ss3082081356 Nov 08, 2017 (151)
71 CSHL ss3343550585 Nov 08, 2017 (151)
72 ILLUMINA ss3626143355 Oct 11, 2018 (152)
73 ILLUMINA ss3630576331 Oct 11, 2018 (152)
74 ILLUMINA ss3637769201 Oct 11, 2018 (152)
75 ILLUMINA ss3641601014 Oct 11, 2018 (152)
76 ILLUMINA ss3642779978 Oct 11, 2018 (152)
77 OMUKHERJEE_ADBS ss3646232667 Oct 11, 2018 (152)
78 URBANLAB ss3646709304 Oct 11, 2018 (152)
79 ILLUMINA ss3653637628 Oct 11, 2018 (152)
80 EGCUT_WGS ss3655225092 Jul 12, 2019 (153)
81 EVA_DECODE ss3687176518 Jul 12, 2019 (153)
82 ACPOP ss3727228848 Jul 12, 2019 (153)
83 EVA ss3746456172 Jul 12, 2019 (153)
84 PACBIO ss3783468110 Jul 12, 2019 (153)
85 PACBIO ss3789117751 Jul 12, 2019 (153)
86 PACBIO ss3793990539 Jul 12, 2019 (153)
87 KHV_HUMAN_GENOMES ss3799462591 Jul 12, 2019 (153)
88 EVA ss3825568414 Apr 25, 2020 (154)
89 EVA ss3826278043 Apr 25, 2020 (154)
90 EVA ss3836528433 Apr 25, 2020 (154)
91 EVA ss3841935739 Apr 25, 2020 (154)
92 SGDP_PRJ ss3849278866 Apr 25, 2020 (154)
93 KRGDB ss3894332348 Apr 25, 2020 (154)
94 KOGIC ss3944906387 Apr 25, 2020 (154)
95 FSA-LAB ss3983936052 Apr 25, 2021 (155)
96 FSA-LAB ss3983936053 Apr 25, 2021 (155)
97 EVA ss3986125806 Apr 25, 2021 (155)
98 EVA ss4016921941 Apr 25, 2021 (155)
99 TOPMED ss4457169140 Apr 25, 2021 (155)
100 TOMMO_GENOMICS ss5144871522 Apr 25, 2021 (155)
101 EVA ss5237162425 Apr 25, 2021 (155)
102 1000Genomes NC_000001.10 - 85561546 Oct 11, 2018 (152)
103 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 85561546 Oct 11, 2018 (152)
104 Genetic variation in the Estonian population NC_000001.10 - 85561546 Oct 11, 2018 (152)
105 The Danish reference pan genome NC_000001.10 - 85561546 Apr 25, 2020 (154)
106 gnomAD - Genomes NC_000001.11 - 85095863 Apr 25, 2021 (155)
107 Genome of the Netherlands Release 5 NC_000001.10 - 85561546 Apr 25, 2020 (154)
108 HapMap NC_000001.11 - 85095863 Apr 25, 2020 (154)
109 KOREAN population from KRGDB NC_000001.10 - 85561546 Apr 25, 2020 (154)
110 Korean Genome Project NC_000001.11 - 85095863 Apr 25, 2020 (154)
111 Medical Genome Project healthy controls from Spanish population NC_000001.10 - 85561546 Apr 25, 2020 (154)
112 Northern Sweden NC_000001.10 - 85561546 Jul 12, 2019 (153)
113 Qatari NC_000001.10 - 85561546 Apr 25, 2020 (154)
114 SGDP_PRJ NC_000001.10 - 85561546 Apr 25, 2020 (154)
115 Siberian NC_000001.10 - 85561546 Apr 25, 2020 (154)
116 8.3KJPN NC_000001.10 - 85561546 Apr 25, 2021 (155)
117 TopMed NC_000001.11 - 85095863 Apr 25, 2021 (155)
118 UK 10K study - Twins NC_000001.10 - 85561546 Oct 11, 2018 (152)
119 A Vietnamese Genetic Variation Database NC_000001.10 - 85561546 Jul 12, 2019 (153)
120 ALFA NC_000001.11 - 85095863 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).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss78399243, ss79016393 NC_000001.8:85273566:T:C NC_000001.11:85095862:T:C (self)
ss76855480, ss87594130, ss108376197, ss110753309, ss118858900, ss163602552, ss164691312, ss166785762, ss198716033, ss205332568, ss253243983, ss275908380, ss284088087, ss290553632, ss482420040, ss1584754240, ss1712349517, ss3642779978 NC_000001.9:85334133:T:C NC_000001.11:85095862:T:C (self)
2470782, 1355328, 963340, 1589021, 586708, 1509742, 27454, 513713, 624925, 1295846, 345177, 2840829, 1355328, 291047, ss218498677, ss230618179, ss238294624, ss483099687, ss535280994, ss554376172, ss648186324, ss780150831, ss781993190, ss835634416, ss975380208, ss1068053449, ss1291721612, ss1425881203, ss1574200498, ss1600609145, ss1643603178, ss1710910702, ss1794671632, ss1918582995, ss1966797306, ss2019812025, ss2147828823, ss2326537048, ss2624417151, ss2632541531, ss2697752181, ss2757515083, ss2984866012, ss2985518380, ss2987147714, ss3343550585, ss3626143355, ss3630576331, ss3637769201, ss3641601014, ss3646232667, ss3653637628, ss3655225092, ss3727228848, ss3746456172, ss3783468110, ss3789117751, ss3793990539, ss3825568414, ss3826278043, ss3836528433, ss3849278866, ss3894332348, ss3983936052, ss3983936053, ss3986125806, ss4016921941, ss5144871522 NC_000001.10:85561545:T:C NC_000001.11:85095862:T:C (self)
17436527, 115950, 1284388, 13085965, 20775475, 7202624616, ss2164223489, ss3023668737, ss3082081356, ss3646709304, ss3687176518, ss3799462591, ss3841935739, ss3944906387, ss4457169140, ss5237162425 NC_000001.11:85095862:T:C NC_000001.11:85095862:T:C (self)
ss11350791 NT_026943.12:1898186:T:C NC_000001.11:85095862:T:C (self)
ss15423874 NT_026943.13:10381719:T:C NC_000001.11:85095862:T:C (self)
ss1080875, ss1081286, ss1883472, ss1884009, ss2629882, ss44123851, ss65761479, ss71644655, ss74855135, ss99224850, ss102759384, ss119363918, ss138027948, ss138874066, ss174239405 NT_032977.9:55533463:T:C NC_000001.11:85095862: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.

No publications for rs709766

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.post596+ae089ad