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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.

rs2278871

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr10:14819402 (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
C>A / C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.183921 (48682/264690, TOPMED)
T=0.107238 (15700/146404, ALFA)
T=0.40587 (11469/28258, 14KJPN) (+ 18 more)
T=0.40686 (6819/16760, 8.3KJPN)
T=0.2583 (1654/6404, 1000G_30x)
T=0.2578 (1291/5008, 1000G)
T=0.0806 (361/4480, Estonian)
T=0.0887 (342/3854, ALSPAC)
T=0.0930 (345/3708, TWINSUK)
T=0.3522 (1032/2930, KOREAN)
T=0.2563 (485/1892, HapMap)
T=0.3499 (641/1832, Korea1K)
T=0.087 (87/998, GoNL)
T=0.312 (246/788, PRJEB37584)
T=0.100 (60/600, NorthernSweden)
T=0.116 (25/216, Qatari)
C=0.458 (98/214, SGDP_PRJ)
T=0.236 (50/212, Vietnamese)
T=0.05 (2/40, GENOME_DK)
C=0.5 (5/10, Siberian)
T=0.5 (5/10, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
CDNF : 3 Prime UTR 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 146404 C=0.892762 A=0.000000, T=0.107238
European Sub 127316 C=0.902314 A=0.000000, T=0.097686
African Sub 5456 C=0.7570 A=0.0000, T=0.2430
African Others Sub 194 C=0.716 A=0.000, T=0.284
African American Sub 5262 C=0.7585 A=0.0000, T=0.2415
Asian Sub 560 C=0.721 A=0.000, T=0.279
East Asian Sub 442 C=0.715 A=0.000, T=0.285
Other Asian Sub 118 C=0.746 A=0.000, T=0.254
Latin American 1 Sub 704 C=0.842 A=0.000, T=0.158
Latin American 2 Sub 6162 C=0.8637 A=0.0000, T=0.1363
South Asian Sub 130 C=0.785 A=0.000, T=0.215
Other Sub 6076 C=0.8680 A=0.0000, T=0.1320


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 C=0.816079 T=0.183921
Allele Frequency Aggregator Total Global 146404 C=0.892762 A=0.000000, T=0.107238
Allele Frequency Aggregator European Sub 127316 C=0.902314 A=0.000000, T=0.097686
Allele Frequency Aggregator Latin American 2 Sub 6162 C=0.8637 A=0.0000, T=0.1363
Allele Frequency Aggregator Other Sub 6076 C=0.8680 A=0.0000, T=0.1320
Allele Frequency Aggregator African Sub 5456 C=0.7570 A=0.0000, T=0.2430
Allele Frequency Aggregator Latin American 1 Sub 704 C=0.842 A=0.000, T=0.158
Allele Frequency Aggregator Asian Sub 560 C=0.721 A=0.000, T=0.279
Allele Frequency Aggregator South Asian Sub 130 C=0.785 A=0.000, T=0.215
14KJPN JAPANESE Study-wide 28258 C=0.59413 T=0.40587
8.3KJPN JAPANESE Study-wide 16760 C=0.59314 T=0.40686
1000Genomes_30x Global Study-wide 6404 C=0.7417 T=0.2583
1000Genomes_30x African Sub 1786 C=0.6467 T=0.3533
1000Genomes_30x Europe Sub 1266 C=0.9107 T=0.0893
1000Genomes_30x South Asian Sub 1202 C=0.6373 T=0.3627
1000Genomes_30x East Asian Sub 1170 C=0.6966 T=0.3034
1000Genomes_30x American Sub 980 C=0.879 T=0.121
1000Genomes Global Study-wide 5008 C=0.7422 T=0.2578
1000Genomes African Sub 1322 C=0.6566 T=0.3434
1000Genomes East Asian Sub 1008 C=0.6974 T=0.3026
1000Genomes Europe Sub 1006 C=0.9155 T=0.0845
1000Genomes South Asian Sub 978 C=0.635 T=0.365
1000Genomes American Sub 694 C=0.870 T=0.130
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.9194 T=0.0806
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.9113 T=0.0887
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.9070 T=0.0930
KOREAN population from KRGDB KOREAN Study-wide 2930 C=0.6478 T=0.3522
HapMap Global Study-wide 1892 C=0.7437 T=0.2563
HapMap American Sub 770 C=0.761 T=0.239
HapMap African Sub 692 C=0.744 T=0.256
HapMap Asian Sub 254 C=0.594 T=0.406
HapMap Europe Sub 176 C=0.881 T=0.119
Korean Genome Project KOREAN Study-wide 1832 C=0.6501 T=0.3499
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 C=0.913 T=0.087
CNV burdens in cranial meningiomas Global Study-wide 788 C=0.688 T=0.312
CNV burdens in cranial meningiomas CRM Sub 788 C=0.688 T=0.312
Northern Sweden ACPOP Study-wide 600 C=0.900 T=0.100
Qatari Global Study-wide 216 C=0.884 T=0.116
SGDP_PRJ Global Study-wide 214 C=0.458 T=0.542
A Vietnamese Genetic Variation Database Global Study-wide 212 C=0.764 T=0.236
The Danish reference pan genome Danish Study-wide 40 C=0.95 T=0.05
Siberian Global Study-wide 10 C=0.5 T=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 10 NC_000010.11:g.14819402C>A
GRCh38.p14 chr 10 NC_000010.11:g.14819402C>T
GRCh37.p13 chr 10 NC_000010.10:g.14861401C>A
GRCh37.p13 chr 10 NC_000010.10:g.14861401C>T
Gene: CDNF, cerebral dopamine neurotrophic factor (minus strand)
Molecule type Change Amino acid[Codon] SO Term
CDNF transcript NM_001029954.3:c.*578= N/A 3 Prime UTR Variant
CDNF transcript variant X1 XM_011519488.3:c.*578= N/A 3 Prime UTR 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 C= A T
GRCh38.p14 chr 10 NC_000010.11:g.14819402= NC_000010.11:g.14819402C>A NC_000010.11:g.14819402C>T
GRCh37.p13 chr 10 NC_000010.10:g.14861401= NC_000010.10:g.14861401C>A NC_000010.10:g.14861401C>T
CDNF transcript variant X1 XM_011519488.3:c.*578= XM_011519488.3:c.*578G>T XM_011519488.3:c.*578G>A
CDNF transcript variant X1 XM_011519488.2:c.*578= XM_011519488.2:c.*578G>T XM_011519488.2:c.*578G>A
CDNF transcript variant X1 XM_011519488.1:c.*578= XM_011519488.1:c.*578G>T XM_011519488.1:c.*578G>A
CDNF transcript NM_001029954.3:c.*578= NM_001029954.3:c.*578G>T NM_001029954.3:c.*578G>A
CDNF transcript NM_001029954.2:c.*578= NM_001029954.2:c.*578G>T NM_001029954.2:c.*578G>A
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, 22 Frequency submissions
No Submitter Submission ID Date (Build)
1 YUSUKE ss3216273 Sep 28, 2001 (100)
2 TSC-CSHL ss4089036 Nov 05, 2001 (101)
3 CSHL-HAPMAP ss17394573 Feb 27, 2004 (120)
4 PERLEGEN ss23245410 Sep 20, 2004 (123)
5 ABI ss38512613 Mar 14, 2006 (126)
6 PERLEGEN ss69071916 May 16, 2007 (127)
7 ILLUMINA ss75107430 Dec 06, 2007 (129)
8 SI_EXO ss76889294 Dec 06, 2007 (129)
9 HGSV ss82020464 Dec 15, 2007 (130)
10 HGSV ss84717053 Dec 15, 2007 (130)
11 BGI ss102857295 Dec 01, 2009 (131)
12 KRIBB_YJKIM ss119426727 Dec 01, 2009 (131)
13 GMI ss154632886 Dec 01, 2009 (131)
14 ILLUMINA ss160527208 Dec 01, 2009 (131)
15 ENSEMBL ss161317293 Dec 01, 2009 (131)
16 COMPLETE_GENOMICS ss170536106 Jul 04, 2010 (132)
17 ILLUMINA ss173242409 Jul 04, 2010 (132)
18 BUSHMAN ss201188402 Jul 04, 2010 (132)
19 1000GENOMES ss224584782 Jul 14, 2010 (132)
20 1000GENOMES ss235070229 Jul 15, 2010 (132)
21 1000GENOMES ss241798988 Jul 15, 2010 (132)
22 GMI ss280495366 May 04, 2012 (137)
23 PJP ss290981633 May 09, 2011 (134)
24 ILLUMINA ss480502368 May 04, 2012 (137)
25 ILLUMINA ss480516714 May 04, 2012 (137)
26 ILLUMINA ss481323159 Sep 08, 2015 (146)
27 ILLUMINA ss485048660 May 04, 2012 (137)
28 ILLUMINA ss537067981 Sep 08, 2015 (146)
29 TISHKOFF ss561792782 Apr 25, 2013 (138)
30 SSMP ss656300842 Apr 25, 2013 (138)
31 ILLUMINA ss778489439 Sep 08, 2015 (146)
32 ILLUMINA ss782970547 Sep 08, 2015 (146)
33 ILLUMINA ss783932119 Sep 08, 2015 (146)
34 ILLUMINA ss832226869 Sep 08, 2015 (146)
35 ILLUMINA ss833945422 Sep 08, 2015 (146)
36 EVA-GONL ss987229586 Aug 21, 2014 (142)
37 JMKIDD_LAB ss1076788664 Aug 21, 2014 (142)
38 1000GENOMES ss1336402529 Aug 21, 2014 (142)
39 EVA_GENOME_DK ss1574942570 Apr 01, 2015 (144)
40 EVA_DECODE ss1596883299 Apr 01, 2015 (144)
41 EVA_UK10K_ALSPAC ss1624058220 Apr 01, 2015 (144)
42 EVA_UK10K_TWINSUK ss1667052253 Apr 01, 2015 (144)
43 EVA_SVP ss1713160750 Apr 01, 2015 (144)
44 ILLUMINA ss1751958608 Sep 08, 2015 (146)
45 HAMMER_LAB ss1806272162 Sep 08, 2015 (146)
46 WEILL_CORNELL_DGM ss1930555483 Feb 12, 2016 (147)
47 GENOMED ss1967068783 Jul 19, 2016 (147)
48 JJLAB ss2026003762 Sep 14, 2016 (149)
49 USC_VALOUEV ss2154248488 Dec 20, 2016 (150)
50 HUMAN_LONGEVITY ss2172915181 Dec 20, 2016 (150)
51 SYSTEMSBIOZJU ss2627472549 Nov 08, 2017 (151)
52 ILLUMINA ss2632680872 Nov 08, 2017 (151)
53 GRF ss2698475549 Nov 08, 2017 (151)
54 GNOMAD ss2885853433 Nov 08, 2017 (151)
55 SWEGEN ss3005990781 Nov 08, 2017 (151)
56 BIOINF_KMB_FNS_UNIBA ss3026787880 Nov 08, 2017 (151)
57 CSHL ss3348979004 Nov 08, 2017 (151)
58 ILLUMINA ss3626395512 Oct 12, 2018 (152)
59 ILLUMINA ss3630708283 Oct 12, 2018 (152)
60 ILLUMINA ss3632940450 Oct 12, 2018 (152)
61 ILLUMINA ss3633637173 Oct 12, 2018 (152)
62 ILLUMINA ss3634392267 Oct 12, 2018 (152)
63 ILLUMINA ss3635329931 Oct 12, 2018 (152)
64 ILLUMINA ss3636072857 Oct 12, 2018 (152)
65 ILLUMINA ss3637080529 Oct 12, 2018 (152)
66 ILLUMINA ss3637836392 Oct 12, 2018 (152)
67 ILLUMINA ss3640099615 Oct 12, 2018 (152)
68 ILLUMINA ss3642840847 Oct 12, 2018 (152)
69 OMUKHERJEE_ADBS ss3646403056 Oct 12, 2018 (152)
70 EGCUT_WGS ss3673519598 Jul 13, 2019 (153)
71 EVA_DECODE ss3689347948 Jul 13, 2019 (153)
72 ACPOP ss3737092384 Jul 13, 2019 (153)
73 ILLUMINA ss3744693161 Jul 13, 2019 (153)
74 EVA ss3747788557 Jul 13, 2019 (153)
75 ILLUMINA ss3772193831 Jul 13, 2019 (153)
76 PACBIO ss3786593375 Jul 13, 2019 (153)
77 PACBIO ss3791784753 Jul 13, 2019 (153)
78 PACBIO ss3796666631 Jul 13, 2019 (153)
79 KHV_HUMAN_GENOMES ss3813148575 Jul 13, 2019 (153)
80 EVA ss3825771656 Apr 26, 2020 (154)
81 EVA ss3831987046 Apr 26, 2020 (154)
82 SGDP_PRJ ss3873603406 Apr 26, 2020 (154)
83 KRGDB ss3921552376 Apr 26, 2020 (154)
84 KOGIC ss3967266892 Apr 26, 2020 (154)
85 EVA ss3984630434 Apr 26, 2021 (155)
86 EVA ss4017472849 Apr 26, 2021 (155)
87 TOPMED ss4843466650 Apr 26, 2021 (155)
88 TOMMO_GENOMICS ss5196408319 Apr 26, 2021 (155)
89 1000G_HIGH_COVERAGE ss5283032560 Oct 16, 2022 (156)
90 EVA ss5315455189 Oct 16, 2022 (156)
91 HUGCELL_USP ss5478799743 Oct 16, 2022 (156)
92 EVA ss5509912061 Oct 16, 2022 (156)
93 1000G_HIGH_COVERAGE ss5576469113 Oct 16, 2022 (156)
94 SANFORD_IMAGENETICS ss5648741075 Oct 16, 2022 (156)
95 TOMMO_GENOMICS ss5741298668 Oct 16, 2022 (156)
96 EVA ss5799805134 Oct 16, 2022 (156)
97 YY_MCH ss5811226601 Oct 16, 2022 (156)
98 EVA ss5824023220 Oct 16, 2022 (156)
99 EVA ss5849453529 Oct 16, 2022 (156)
100 EVA ss5877865399 Oct 16, 2022 (156)
101 EVA ss5940028941 Oct 16, 2022 (156)
102 1000Genomes NC_000010.10 - 14861401 Oct 12, 2018 (152)
103 1000Genomes_30x NC_000010.11 - 14819402 Oct 16, 2022 (156)
104 The Avon Longitudinal Study of Parents and Children NC_000010.10 - 14861401 Oct 12, 2018 (152)
105 Genetic variation in the Estonian population NC_000010.10 - 14861401 Oct 12, 2018 (152)
106 The Danish reference pan genome NC_000010.10 - 14861401 Apr 26, 2020 (154)
107 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 344319036 (NC_000010.11:14819401:C:A 1/140050)
Row 344319037 (NC_000010.11:14819401:C:T 23709/140014)

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

Submission ignored due to conflicting rows:
Row 344319036 (NC_000010.11:14819401:C:A 1/140050)
Row 344319037 (NC_000010.11:14819401:C:T 23709/140014)

- Apr 26, 2021 (155)
109 Genome of the Netherlands Release 5 NC_000010.10 - 14861401 Apr 26, 2020 (154)
110 HapMap NC_000010.11 - 14819402 Apr 26, 2020 (154)
111 KOREAN population from KRGDB NC_000010.10 - 14861401 Apr 26, 2020 (154)
112 Korean Genome Project NC_000010.11 - 14819402 Apr 26, 2020 (154)
113 Northern Sweden NC_000010.10 - 14861401 Jul 13, 2019 (153)
114 CNV burdens in cranial meningiomas NC_000010.10 - 14861401 Apr 26, 2021 (155)
115 Qatari NC_000010.10 - 14861401 Apr 26, 2020 (154)
116 SGDP_PRJ NC_000010.10 - 14861401 Apr 26, 2020 (154)
117 Siberian NC_000010.10 - 14861401 Apr 26, 2020 (154)
118 8.3KJPN NC_000010.10 - 14861401 Apr 26, 2021 (155)
119 14KJPN NC_000010.11 - 14819402 Oct 16, 2022 (156)
120 TopMed NC_000010.11 - 14819402 Apr 26, 2021 (155)
121 UK 10K study - Twins NC_000010.10 - 14861401 Oct 12, 2018 (152)
122 A Vietnamese Genetic Variation Database NC_000010.10 - 14861401 Jul 13, 2019 (153)
123 ALFA NC_000010.11 - 14819402 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)
rs60708022 May 26, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
5756247996 NC_000010.11:14819401:C:A NC_000010.11:14819401:C:A (self)
ss82020464, ss84717053 NC_000010.8:14901406:C:T NC_000010.11:14819401:C:T (self)
ss170536106, ss201188402, ss280495366, ss290981633, ss480502368, ss1596883299, ss1713160750, ss3642840847 NC_000010.9:14901406:C:T NC_000010.11:14819401:C:T (self)
48753470, 27093541, 19257846, 2046833, 12082422, 28729770, 10377249, 179890, 12597413, 25620386, 6764842, 54377626, 27093541, 6015532, ss224584782, ss235070229, ss241798988, ss480516714, ss481323159, ss485048660, ss537067981, ss561792782, ss656300842, ss778489439, ss782970547, ss783932119, ss832226869, ss833945422, ss987229586, ss1076788664, ss1336402529, ss1574942570, ss1624058220, ss1667052253, ss1751958608, ss1806272162, ss1930555483, ss1967068783, ss2026003762, ss2154248488, ss2627472549, ss2632680872, ss2698475549, ss2885853433, ss3005990781, ss3348979004, ss3626395512, ss3630708283, ss3632940450, ss3633637173, ss3634392267, ss3635329931, ss3636072857, ss3637080529, ss3637836392, ss3640099615, ss3646403056, ss3673519598, ss3737092384, ss3744693161, ss3747788557, ss3772193831, ss3786593375, ss3791784753, ss3796666631, ss3825771656, ss3831987046, ss3873603406, ss3921552376, ss3984630434, ss4017472849, ss5196408319, ss5315455189, ss5509912061, ss5648741075, ss5799805134, ss5824023220, ss5940028941 NC_000010.10:14861400:C:T NC_000010.11:14819401:C:T (self)
63995048, 347005, 23644893, 75135772, 59012305, 5756247996, ss2172915181, ss3026787880, ss3689347948, ss3813148575, ss3967266892, ss4843466650, ss5283032560, ss5478799743, ss5576469113, ss5741298668, ss5811226601, ss5849453529, ss5877865399 NC_000010.11:14819401:C:T NC_000010.11:14819401:C:T (self)
ss3216273, ss4089036, ss23245410, ss38512613, ss69071916, ss75107430, ss102857295, ss119426727, ss154632886, ss160527208, ss161317293, ss173242409 NT_008705.16:14801400:C:T NC_000010.11:14819401:C:T (self)
ss17394573, ss76889294 NT_077569.2:9224296:C:T NC_000010.11:14819401:C:T (self)
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 rs2278871
PMID Title Author Year Journal
19429035 Association analysis between polymorphisms in the conserved dopamine neurotrophic factor (CDNF) gene and cocaine dependence. Lohoff FW et al. 2009 Neuroscience letters
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