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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.

rs10865016

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr2:98372841 (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 / G>C / G>T
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.232623 (61573/264690, TOPMED)
A=0.39245 (11089/28256, 14KJPN)
A=0.11302 (1937/17138, ALFA) (+ 17 more)
A=0.39135 (6559/16760, 8.3KJPN)
A=0.2416 (1547/6404, 1000G_30x)
A=0.2420 (1212/5008, 1000G)
A=0.2031 (910/4480, Estonian)
A=0.1866 (719/3854, ALSPAC)
A=0.1804 (669/3708, TWINSUK)
A=0.4024 (1179/2930, KOREAN)
A=0.3974 (728/1832, Korea1K)
A=0.172 (172/998, GoNL)
A=0.372 (295/792, PRJEB37584)
A=0.115 (69/600, NorthernSweden)
A=0.226 (74/328, HapMap)
G=0.375 (96/256, SGDP_PRJ)
A=0.278 (60/216, Qatari)
A=0.278 (59/212, Vietnamese)
A=0.15 (6/40, GENOME_DK)
G=0.38 (13/34, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
CNGA3 : Intron Variant
Publications
1 citation
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 17138 G=0.88698 A=0.11302, C=0.00000, T=0.00000
European Sub 11596 G=0.88298 A=0.11702, C=0.00000, T=0.00000
African Sub 4584 G=0.8874 A=0.1126, C=0.0000, T=0.0000
African Others Sub 168 G=0.905 A=0.095, C=0.000, T=0.000
African American Sub 4416 G=0.8868 A=0.1132, C=0.0000, T=0.0000
Asian Sub 52 G=0.98 A=0.02, C=0.00, T=0.00
East Asian Sub 40 G=1.00 A=0.00, C=0.00, T=0.00
Other Asian Sub 12 G=0.92 A=0.08, C=0.00, T=0.00
Latin American 1 Sub 78 G=1.00 A=0.00, C=0.00, T=0.00
Latin American 2 Sub 186 G=1.000 A=0.000, C=0.000, T=0.000
South Asian Sub 78 G=1.00 A=0.00, C=0.00, T=0.00
Other Sub 564 G=0.888 A=0.112, C=0.000, T=0.000


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=0.767377 A=0.232623
14KJPN JAPANESE Study-wide 28256 G=0.60755 A=0.39245
Allele Frequency Aggregator Total Global 17138 G=0.88698 A=0.11302, C=0.00000, T=0.00000
Allele Frequency Aggregator European Sub 11596 G=0.88298 A=0.11702, C=0.00000, T=0.00000
Allele Frequency Aggregator African Sub 4584 G=0.8874 A=0.1126, C=0.0000, T=0.0000
Allele Frequency Aggregator Other Sub 564 G=0.888 A=0.112, C=0.000, T=0.000
Allele Frequency Aggregator Latin American 2 Sub 186 G=1.000 A=0.000, C=0.000, T=0.000
Allele Frequency Aggregator Latin American 1 Sub 78 G=1.00 A=0.00, C=0.00, T=0.00
Allele Frequency Aggregator South Asian Sub 78 G=1.00 A=0.00, C=0.00, T=0.00
Allele Frequency Aggregator Asian Sub 52 G=0.98 A=0.02, C=0.00, T=0.00
8.3KJPN JAPANESE Study-wide 16760 G=0.60865 A=0.39135
1000Genomes_30x Global Study-wide 6404 G=0.7584 A=0.2416
1000Genomes_30x African Sub 1786 G=0.8130 A=0.1870
1000Genomes_30x Europe Sub 1266 G=0.7970 A=0.2030
1000Genomes_30x South Asian Sub 1202 G=0.8295 A=0.1705
1000Genomes_30x East Asian Sub 1170 G=0.6761 A=0.3239
1000Genomes_30x American Sub 980 G=0.620 A=0.380
1000Genomes Global Study-wide 5008 G=0.7580 A=0.2420
1000Genomes African Sub 1322 G=0.8147 A=0.1853
1000Genomes East Asian Sub 1008 G=0.6766 A=0.3234
1000Genomes Europe Sub 1006 G=0.7903 A=0.2097
1000Genomes South Asian Sub 978 G=0.831 A=0.169
1000Genomes American Sub 694 G=0.618 A=0.382
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.7969 A=0.2031
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.8134 A=0.1866
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.8196 A=0.1804
KOREAN population from KRGDB KOREAN Study-wide 2930 G=0.5976 A=0.4024
Korean Genome Project KOREAN Study-wide 1832 G=0.6026 A=0.3974
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.828 A=0.172
CNV burdens in cranial meningiomas Global Study-wide 792 G=0.628 A=0.372
CNV burdens in cranial meningiomas CRM Sub 792 G=0.628 A=0.372
Northern Sweden ACPOP Study-wide 600 G=0.885 A=0.115
HapMap Global Study-wide 328 G=0.774 A=0.226
HapMap African Sub 120 G=0.842 A=0.158
HapMap American Sub 118 G=0.831 A=0.169
HapMap Asian Sub 90 G=0.61 A=0.39
SGDP_PRJ Global Study-wide 256 G=0.375 A=0.625
Qatari Global Study-wide 216 G=0.722 A=0.278
A Vietnamese Genetic Variation Database Global Study-wide 212 G=0.722 A=0.278
The Danish reference pan genome Danish Study-wide 40 G=0.85 A=0.15
Siberian Global Study-wide 34 G=0.38 A=0.62
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 2 NC_000002.12:g.98372841G>A
GRCh38.p14 chr 2 NC_000002.12:g.98372841G>C
GRCh38.p14 chr 2 NC_000002.12:g.98372841G>T
GRCh37.p13 chr 2 NC_000002.11:g.98989304G>A
GRCh37.p13 chr 2 NC_000002.11:g.98989304G>C
GRCh37.p13 chr 2 NC_000002.11:g.98989304G>T
CNGA3 RefSeqGene NG_009097.1:g.31687G>A
CNGA3 RefSeqGene NG_009097.1:g.31687G>C
CNGA3 RefSeqGene NG_009097.1:g.31687G>T
Gene: CNGA3, cyclic nucleotide gated channel subunit alpha 3 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
CNGA3 transcript variant 2 NM_001079878.2:c.101+2765…

NM_001079878.2:c.101+2765G>A

N/A Intron Variant
CNGA3 transcript variant 1 NM_001298.3:c.101+2765G>A N/A Intron Variant
CNGA3 transcript variant X3 XM_006712243.3:c.101+2765…

XM_006712243.3:c.101+2765G>A

N/A Intron Variant
CNGA3 transcript variant X2 XM_011510554.3:c.101+2765…

XM_011510554.3:c.101+2765G>A

N/A Intron Variant
CNGA3 transcript variant X1 XM_047443222.1:c.101+2765…

XM_047443222.1:c.101+2765G>A

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 C T
GRCh38.p14 chr 2 NC_000002.12:g.98372841= NC_000002.12:g.98372841G>A NC_000002.12:g.98372841G>C NC_000002.12:g.98372841G>T
GRCh37.p13 chr 2 NC_000002.11:g.98989304= NC_000002.11:g.98989304G>A NC_000002.11:g.98989304G>C NC_000002.11:g.98989304G>T
CNGA3 RefSeqGene NG_009097.1:g.31687= NG_009097.1:g.31687G>A NG_009097.1:g.31687G>C NG_009097.1:g.31687G>T
CNGA3 transcript variant 2 NM_001079878.1:c.101+2765= NM_001079878.1:c.101+2765G>A NM_001079878.1:c.101+2765G>C NM_001079878.1:c.101+2765G>T
CNGA3 transcript variant 2 NM_001079878.2:c.101+2765= NM_001079878.2:c.101+2765G>A NM_001079878.2:c.101+2765G>C NM_001079878.2:c.101+2765G>T
CNGA3 transcript variant 1 NM_001298.2:c.101+2765= NM_001298.2:c.101+2765G>A NM_001298.2:c.101+2765G>C NM_001298.2:c.101+2765G>T
CNGA3 transcript variant 1 NM_001298.3:c.101+2765= NM_001298.3:c.101+2765G>A NM_001298.3:c.101+2765G>C NM_001298.3:c.101+2765G>T
CNGA3 transcript variant X1 XM_005263868.1:c.101+2765= XM_005263868.1:c.101+2765G>A XM_005263868.1:c.101+2765G>C XM_005263868.1:c.101+2765G>T
CNGA3 transcript variant X3 XM_006712243.3:c.101+2765= XM_006712243.3:c.101+2765G>A XM_006712243.3:c.101+2765G>C XM_006712243.3:c.101+2765G>T
CNGA3 transcript variant X2 XM_011510554.3:c.101+2765= XM_011510554.3:c.101+2765G>A XM_011510554.3:c.101+2765G>C XM_011510554.3:c.101+2765G>T
CNGA3 transcript variant X1 XM_047443222.1:c.101+2765= XM_047443222.1:c.101+2765G>A XM_047443222.1:c.101+2765G>C XM_047443222.1:c.101+2765G>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#.

67 SubSNP, 22 Frequency submissions
No Submitter Submission ID Date (Build)
1 CSHL-HAPMAP ss16865920 Feb 27, 2004 (120)
2 CSHL-HAPMAP ss17673854 Feb 27, 2004 (120)
3 CSHL-HAPMAP ss20108518 Feb 27, 2004 (120)
4 PERLEGEN ss23929264 Sep 20, 2004 (123)
5 ABI ss44197831 Mar 14, 2006 (126)
6 PERLEGEN ss68822290 May 18, 2007 (127)
7 1000GENOMES ss109717542 Jan 24, 2009 (130)
8 GMI ss157401761 Dec 01, 2009 (131)
9 ENSEMBL ss161302339 Dec 01, 2009 (131)
10 COMPLETE_GENOMICS ss166910423 Jul 04, 2010 (132)
11 BUSHMAN ss200781948 Jul 04, 2010 (132)
12 BCM-HGSC-SUB ss205803852 Jul 04, 2010 (132)
13 1000GENOMES ss219391062 Jul 14, 2010 (132)
14 1000GENOMES ss231276186 Jul 14, 2010 (132)
15 1000GENOMES ss238804432 Jul 15, 2010 (132)
16 BL ss253314002 May 09, 2011 (134)
17 GMI ss276589071 May 04, 2012 (137)
18 GMI ss284396604 Apr 25, 2013 (138)
19 TISHKOFF ss555736638 Apr 25, 2013 (138)
20 SSMP ss649351261 Apr 25, 2013 (138)
21 EVA-GONL ss977125519 Aug 21, 2014 (142)
22 JMKIDD_LAB ss1069327369 Aug 21, 2014 (142)
23 1000GENOMES ss1298411183 Aug 21, 2014 (142)
24 DDI ss1428666180 Apr 01, 2015 (144)
25 EVA_GENOME_DK ss1578992450 Apr 01, 2015 (144)
26 EVA_DECODE ss1586546725 Apr 01, 2015 (144)
27 EVA_UK10K_ALSPAC ss1604098591 Apr 01, 2015 (144)
28 EVA_UK10K_TWINSUK ss1647092624 Apr 01, 2015 (144)
29 HAMMER_LAB ss1797150642 Sep 08, 2015 (146)
30 WEILL_CORNELL_DGM ss1920370806 Feb 12, 2016 (147)
31 GENOMED ss1968834344 Jul 19, 2016 (147)
32 JJLAB ss2020715072 Sep 14, 2016 (149)
33 USC_VALOUEV ss2148770430 Dec 20, 2016 (150)
34 HUMAN_LONGEVITY ss2232536332 Dec 20, 2016 (150)
35 SYSTEMSBIOZJU ss2624863217 Nov 08, 2017 (151)
36 GRF ss2703371911 Nov 08, 2017 (151)
37 GNOMAD ss2776996272 Nov 08, 2017 (151)
38 AFFY ss2985802004 Nov 08, 2017 (151)
39 SWEGEN ss2990034596 Nov 08, 2017 (151)
40 BIOINF_KMB_FNS_UNIBA ss3024120160 Nov 08, 2017 (151)
41 CSHL ss3344368526 Nov 08, 2017 (151)
42 EGCUT_WGS ss3657922520 Jul 13, 2019 (153)
43 EVA_DECODE ss3704458443 Jul 13, 2019 (153)
44 ACPOP ss3728672691 Jul 13, 2019 (153)
45 EVA ss3757103655 Jul 13, 2019 (153)
46 KHV_HUMAN_GENOMES ss3801473827 Jul 13, 2019 (153)
47 EVA ss3827112653 Apr 25, 2020 (154)
48 EVA ss3836967343 Apr 25, 2020 (154)
49 EVA ss3842385680 Apr 25, 2020 (154)
50 SGDP_PRJ ss3852912655 Apr 25, 2020 (154)
51 KRGDB ss3898437096 Apr 25, 2020 (154)
52 KOGIC ss3948500963 Apr 25, 2020 (154)
53 EVA ss3984486473 Apr 26, 2021 (155)
54 TOPMED ss4516039619 Apr 26, 2021 (155)
55 TOMMO_GENOMICS ss5152794662 Apr 26, 2021 (155)
56 1000G_HIGH_COVERAGE ss5249194338 Oct 12, 2022 (156)
57 EVA ss5330838846 Oct 12, 2022 (156)
58 HUGCELL_USP ss5449141165 Oct 12, 2022 (156)
59 1000G_HIGH_COVERAGE ss5525039002 Oct 12, 2022 (156)
60 SANFORD_IMAGENETICS ss5624451993 Oct 12, 2022 (156)
61 SANFORD_IMAGENETICS ss5629336389 Oct 12, 2022 (156)
62 TOMMO_GENOMICS ss5682606471 Oct 12, 2022 (156)
63 YY_MCH ss5802521599 Oct 12, 2022 (156)
64 EVA ss5820489243 Oct 12, 2022 (156)
65 EVA ss5852627963 Oct 12, 2022 (156)
66 EVA ss5931488395 Oct 12, 2022 (156)
67 EVA ss5955546818 Oct 12, 2022 (156)
68 1000Genomes NC_000002.11 - 98989304 Oct 11, 2018 (152)
69 1000Genomes_30x NC_000002.12 - 98372841 Oct 12, 2022 (156)
70 The Avon Longitudinal Study of Parents and Children NC_000002.11 - 98989304 Oct 11, 2018 (152)
71 Genetic variation in the Estonian population NC_000002.11 - 98989304 Oct 11, 2018 (152)
72 The Danish reference pan genome NC_000002.11 - 98989304 Apr 25, 2020 (154)
73 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 67104384 (NC_000002.12:98372840:G:A 29552/139914)
Row 67104385 (NC_000002.12:98372840:G:T 3/139976)

- Apr 26, 2021 (155)
74 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 67104384 (NC_000002.12:98372840:G:A 29552/139914)
Row 67104385 (NC_000002.12:98372840:G:T 3/139976)

- Apr 26, 2021 (155)
75 Genome of the Netherlands Release 5 NC_000002.11 - 98989304 Apr 25, 2020 (154)
76 HapMap NC_000002.12 - 98372841 Apr 25, 2020 (154)
77 KOREAN population from KRGDB NC_000002.11 - 98989304 Apr 25, 2020 (154)
78 Korean Genome Project NC_000002.12 - 98372841 Apr 25, 2020 (154)
79 Northern Sweden NC_000002.11 - 98989304 Jul 13, 2019 (153)
80 CNV burdens in cranial meningiomas NC_000002.11 - 98989304 Apr 26, 2021 (155)
81 Qatari NC_000002.11 - 98989304 Apr 25, 2020 (154)
82 SGDP_PRJ NC_000002.11 - 98989304 Apr 25, 2020 (154)
83 Siberian NC_000002.11 - 98989304 Apr 25, 2020 (154)
84 8.3KJPN NC_000002.11 - 98989304 Apr 26, 2021 (155)
85 14KJPN NC_000002.12 - 98372841 Oct 12, 2022 (156)
86 TopMed NC_000002.12 - 98372841 Apr 26, 2021 (155)
87 UK 10K study - Twins NC_000002.11 - 98989304 Oct 11, 2018 (152)
88 A Vietnamese Genetic Variation Database NC_000002.11 - 98989304 Jul 13, 2019 (153)
89 ALFA NC_000002.12 - 98372841 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
ss109717542, ss166910423, ss200781948, ss205803852, ss253314002, ss276589071, ss284396604, ss1586546725 NC_000002.10:98355735:G:A NC_000002.12:98372840:G:A (self)
9395616, 5185464, 3660768, 5160353, 2279754, 5614490, 1957556, 35807, 2412736, 4929635, 1286784, 10763969, 5185464, 1125302, ss219391062, ss231276186, ss238804432, ss555736638, ss649351261, ss977125519, ss1069327369, ss1298411183, ss1428666180, ss1578992450, ss1604098591, ss1647092624, ss1797150642, ss1920370806, ss1968834344, ss2020715072, ss2148770430, ss2624863217, ss2703371911, ss2776996272, ss2985802004, ss2990034596, ss3344368526, ss3657922520, ss3728672691, ss3757103655, ss3827112653, ss3836967343, ss3852912655, ss3898437096, ss3984486473, ss5152794662, ss5330838846, ss5624451993, ss5629336389, ss5820489243, ss5955546818 NC_000002.11:98989303:G:A NC_000002.12:98372840:G:A (self)
12564937, 1850809, 4878964, 16443575, 319862498, 9163804793, ss2232536332, ss3024120160, ss3704458443, ss3801473827, ss3842385680, ss3948500963, ss4516039619, ss5249194338, ss5449141165, ss5525039002, ss5682606471, ss5802521599, ss5852627963, ss5931488395 NC_000002.12:98372840:G:A NC_000002.12:98372840:G:A (self)
ss16865920, ss17673854, ss20108518 NT_022171.13:1055327:G:A NC_000002.12:98372840:G:A (self)
ss23929264, ss44197831, ss68822290, ss157401761, ss161302339 NT_022171.15:3663132:G:A NC_000002.12:98372840:G:A (self)
9163804793 NC_000002.12:98372840:G:C NC_000002.12:98372840:G:C (self)
9163804793 NC_000002.12:98372840:G:T NC_000002.12:98372840:G:T (self)
Removed from this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Destination RSIDs
ss2398708633 NC_000002.11:98989303:G:T NC_000002.12:98372840:G:T
Help

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

1 citation for rs10865016
PMID Title Author Year Journal
19268276 Genome-wide association study of smoking initiation and current smoking. Vink JM et al. 2009 American journal of human genetics
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