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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.

rs1502223

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr18:53498146 (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
C=0.239004 (63262/264690, TOPMED)
C=0.276248 (41246/149308, ALFA)
C=0.233396 (32716/140174, GnomAD) (+ 15 more)
C=0.45984 (7707/16760, 8.3KJPN)
C=0.2911 (1458/5008, 1000G)
C=0.2096 (939/4480, Estonian)
C=0.2916 (1124/3854, ALSPAC)
C=0.2888 (1071/3708, TWINSUK)
C=0.4317 (1265/2930, KOREAN)
C=0.2654 (500/1884, HapMap)
C=0.4170 (764/1832, Korea1K)
C=0.301 (300/998, GoNL)
C=0.287 (172/600, NorthernSweden)
T=0.417 (126/302, SGDP_PRJ)
C=0.241 (52/216, Qatari)
C=0.393 (84/214, Vietnamese)
C=0.35 (14/40, GENOME_DK)
T=0.33 (6/18, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
DCC : 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 18 NC_000018.10:g.53498146T>C
GRCh37.p13 chr 18 NC_000018.9:g.51024516T>C
DCC RefSeqGene (LRG_1107) NG_013341.2:g.1162975T>C
Gene: DCC, DCC netrin 1 receptor (plus strand)
Molecule type Change Amino acid[Codon] SO Term
DCC transcript NM_005215.4:c.3899-1152T>C N/A Intron Variant
DCC transcript variant X2 XM_011525843.1:c.3899-115…

XM_011525843.1:c.3899-1152T>C

N/A Intron Variant
DCC transcript variant X5 XM_011525844.2:c.2864-115…

XM_011525844.2:c.2864-1152T>C

N/A Intron Variant
DCC transcript variant X1 XM_017025568.1:c.3893-115…

XM_017025568.1:c.3893-1152T>C

N/A Intron Variant
DCC transcript variant X3 XM_017025569.1:c.3839-115…

XM_017025569.1:c.3839-1152T>C

N/A Intron Variant
DCC transcript variant X4 XM_017025570.1:c.2864-115…

XM_017025570.1:c.2864-1152T>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 (New)
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 149308 T=0.723752 C=0.276248
European Sub 128542 T=0.718045 C=0.281955
African Sub 6676 T=0.8736 C=0.1264
African Others Sub 242 T=0.930 C=0.070
African American Sub 6434 T=0.8715 C=0.1285
Asian Sub 630 T=0.567 C=0.433
East Asian Sub 498 T=0.552 C=0.448
Other Asian Sub 132 T=0.621 C=0.379
Latin American 1 Sub 750 T=0.764 C=0.236
Latin American 2 Sub 6290 T=0.6968 C=0.3032
South Asian Sub 184 T=0.663 C=0.337
Other Sub 6236 T=0.7210 C=0.2790


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=0.760996 C=0.239004
gnomAD - Genomes Global Study-wide 140174 T=0.766604 C=0.233396
gnomAD - Genomes European Sub 75900 T=0.73029 C=0.26971
gnomAD - Genomes African Sub 42026 T=0.86739 C=0.13261
gnomAD - Genomes American Sub 13644 T=0.72537 C=0.27463
gnomAD - Genomes Ashkenazi Jewish Sub 3324 T=0.6748 C=0.3252
gnomAD - Genomes East Asian Sub 3128 T=0.5895 C=0.4105
gnomAD - Genomes Other Sub 2152 T=0.7398 C=0.2602
8.3KJPN JAPANESE Study-wide 16760 T=0.54016 C=0.45984
1000Genomes Global Study-wide 5008 T=0.7089 C=0.2911
1000Genomes African Sub 1322 T=0.9009 C=0.0991
1000Genomes East Asian Sub 1008 T=0.5744 C=0.4256
1000Genomes Europe Sub 1006 T=0.7117 C=0.2883
1000Genomes South Asian Sub 978 T=0.572 C=0.428
1000Genomes American Sub 694 T=0.728 C=0.272
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.7904 C=0.2096
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.7084 C=0.2916
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.7112 C=0.2888
KOREAN population from KRGDB KOREAN Study-wide 2930 T=0.5683 C=0.4317
HapMap Global Study-wide 1884 T=0.7346 C=0.2654
HapMap American Sub 766 T=0.663 C=0.337
HapMap African Sub 692 T=0.908 C=0.092
HapMap Asian Sub 252 T=0.528 C=0.472
HapMap Europe Sub 174 T=0.661 C=0.339
Korean Genome Project KOREAN Study-wide 1832 T=0.5830 C=0.4170
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 T=0.699 C=0.301
Northern Sweden ACPOP Study-wide 600 T=0.713 C=0.287
SGDP_PRJ Global Study-wide 302 T=0.417 C=0.583
Qatari Global Study-wide 216 T=0.759 C=0.241
A Vietnamese Genetic Variation Database Global Study-wide 214 T=0.607 C=0.393
The Danish reference pan genome Danish Study-wide 40 T=0.65 C=0.35
Siberian Global Study-wide 18 T=0.33 C=0.67
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 18 NC_000018.10:g.53498146= NC_000018.10:g.53498146T>C
GRCh37.p13 chr 18 NC_000018.9:g.51024516= NC_000018.9:g.51024516T>C
DCC RefSeqGene (LRG_1107) NG_013341.2:g.1162975= NG_013341.2:g.1162975T>C
DCC transcript NM_005215.3:c.3899-1152= NM_005215.3:c.3899-1152T>C
DCC transcript NM_005215.4:c.3899-1152= NM_005215.4:c.3899-1152T>C
DCC transcript variant X1 XM_005258204.1:c.3899-1152= XM_005258204.1:c.3899-1152T>C
DCC transcript variant X2 XM_011525843.1:c.3899-1152= XM_011525843.1:c.3899-1152T>C
DCC transcript variant X5 XM_011525844.2:c.2864-1152= XM_011525844.2:c.2864-1152T>C
DCC transcript variant X1 XM_017025568.1:c.3893-1152= XM_017025568.1:c.3893-1152T>C
DCC transcript variant X3 XM_017025569.1:c.3839-1152= XM_017025569.1:c.3839-1152T>C
DCC transcript variant X4 XM_017025570.1:c.2864-1152= XM_017025570.1:c.2864-1152T>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#.

77 SubSNP, 18 Frequency submissions
No Submitter Submission ID Date (Build)
1 TSC-CSHL ss2333105 Oct 23, 2000 (88)
2 WI_SSAHASNP ss14411807 Dec 05, 2003 (119)
3 PERLEGEN ss24090954 Sep 20, 2004 (123)
4 ILLUMINA ss65789682 Oct 16, 2006 (127)
5 ILLUMINA ss74855133 Dec 07, 2007 (129)
6 BGI ss106547125 Feb 04, 2009 (130)
7 1000GENOMES ss110568787 Jan 25, 2009 (130)
8 KRIBB_YJKIM ss119395711 Dec 01, 2009 (131)
9 ILLUMINA ss160363365 Dec 01, 2009 (131)
10 ILLUMINA ss172544893 Jul 04, 2010 (132)
11 1000GENOMES ss227881962 Jul 14, 2010 (132)
12 1000GENOMES ss237482352 Jul 15, 2010 (132)
13 1000GENOMES ss243728956 Jul 15, 2010 (132)
14 BL ss255678890 May 09, 2011 (134)
15 GMI ss283006047 May 04, 2012 (137)
16 GMI ss287289156 Apr 25, 2013 (138)
17 ILLUMINA ss480004849 May 04, 2012 (137)
18 ILLUMINA ss480013548 May 04, 2012 (137)
19 ILLUMINA ss480671076 Sep 08, 2015 (146)
20 ILLUMINA ss484800513 May 04, 2012 (137)
21 ILLUMINA ss536883222 Sep 08, 2015 (146)
22 TISHKOFF ss565666129 Apr 25, 2013 (138)
23 SSMP ss661500330 Apr 25, 2013 (138)
24 ILLUMINA ss778435563 Aug 21, 2014 (142)
25 ILLUMINA ss782846890 Aug 21, 2014 (142)
26 ILLUMINA ss783811485 Aug 21, 2014 (142)
27 ILLUMINA ss832100705 Apr 01, 2015 (144)
28 ILLUMINA ss833891061 Aug 21, 2014 (142)
29 EVA-GONL ss993771351 Aug 21, 2014 (142)
30 JMKIDD_LAB ss1081532149 Aug 21, 2014 (142)
31 1000GENOMES ss1361194898 Aug 21, 2014 (142)
32 DDI ss1428230250 Apr 01, 2015 (144)
33 EVA_GENOME_DK ss1578421446 Apr 01, 2015 (144)
34 EVA_UK10K_ALSPAC ss1636967255 Apr 01, 2015 (144)
35 EVA_UK10K_TWINSUK ss1679961288 Apr 01, 2015 (144)
36 EVA_DECODE ss1697832461 Apr 01, 2015 (144)
37 EVA_SVP ss1713629287 Apr 01, 2015 (144)
38 ILLUMINA ss1752259738 Sep 08, 2015 (146)
39 WEILL_CORNELL_DGM ss1937239029 Feb 12, 2016 (147)
40 GENOMED ss1968533639 Jul 19, 2016 (147)
41 JJLAB ss2029389325 Sep 14, 2016 (149)
42 USC_VALOUEV ss2157896360 Dec 20, 2016 (150)
43 HUMAN_LONGEVITY ss2221924290 Dec 20, 2016 (150)
44 TOPMED ss2387323785 Dec 20, 2016 (150)
45 SYSTEMSBIOZJU ss2629192628 Nov 08, 2017 (151)
46 ILLUMINA ss2633478187 Nov 08, 2017 (151)
47 GRF ss2702486493 Nov 08, 2017 (151)
48 GNOMAD ss2957162451 Nov 08, 2017 (151)
49 SWEGEN ss3016594611 Nov 08, 2017 (151)
50 BIOINF_KMB_FNS_UNIBA ss3028523829 Nov 08, 2017 (151)
51 TOPMED ss3280393415 Nov 08, 2017 (151)
52 CSHL ss3352042406 Nov 08, 2017 (151)
53 ILLUMINA ss3627818766 Oct 12, 2018 (152)
54 ILLUMINA ss3631454583 Oct 12, 2018 (152)
55 ILLUMINA ss3633164084 Oct 12, 2018 (152)
56 ILLUMINA ss3633872929 Oct 12, 2018 (152)
57 ILLUMINA ss3634707921 Oct 12, 2018 (152)
58 ILLUMINA ss3635560178 Oct 12, 2018 (152)
59 ILLUMINA ss3636397309 Oct 12, 2018 (152)
60 ILLUMINA ss3637311795 Oct 12, 2018 (152)
61 ILLUMINA ss3638198497 Oct 12, 2018 (152)
62 ILLUMINA ss3640415229 Oct 12, 2018 (152)
63 ILLUMINA ss3643174043 Oct 12, 2018 (152)
64 EGCUT_WGS ss3683438996 Jul 13, 2019 (153)
65 EVA_DECODE ss3701742813 Jul 13, 2019 (153)
66 ACPOP ss3742579540 Jul 13, 2019 (153)
67 ILLUMINA ss3745008064 Jul 13, 2019 (153)
68 EVA ss3755443218 Jul 13, 2019 (153)
69 ILLUMINA ss3772505537 Jul 13, 2019 (153)
70 KHV_HUMAN_GENOMES ss3820700214 Jul 13, 2019 (153)
71 EVA ss3835190345 Apr 27, 2020 (154)
72 SGDP_PRJ ss3887106223 Apr 27, 2020 (154)
73 KRGDB ss3936987683 Apr 27, 2020 (154)
74 KOGIC ss3980228195 Apr 27, 2020 (154)
75 EVA ss4017800385 Apr 27, 2021 (155)
76 TOPMED ss5058193430 Apr 27, 2021 (155)
77 TOMMO_GENOMICS ss5225361237 Apr 27, 2021 (155)
78 1000Genomes NC_000018.9 - 51024516 Oct 12, 2018 (152)
79 The Avon Longitudinal Study of Parents and Children NC_000018.9 - 51024516 Oct 12, 2018 (152)
80 Genetic variation in the Estonian population NC_000018.9 - 51024516 Oct 12, 2018 (152)
81 The Danish reference pan genome NC_000018.9 - 51024516 Apr 27, 2020 (154)
82 gnomAD - Genomes NC_000018.10 - 53498146 Apr 27, 2021 (155)
83 Genome of the Netherlands Release 5 NC_000018.9 - 51024516 Apr 27, 2020 (154)
84 HapMap NC_000018.10 - 53498146 Apr 27, 2020 (154)
85 KOREAN population from KRGDB NC_000018.9 - 51024516 Apr 27, 2020 (154)
86 Korean Genome Project NC_000018.10 - 53498146 Apr 27, 2020 (154)
87 Northern Sweden NC_000018.9 - 51024516 Jul 13, 2019 (153)
88 Qatari NC_000018.9 - 51024516 Apr 27, 2020 (154)
89 SGDP_PRJ NC_000018.9 - 51024516 Apr 27, 2020 (154)
90 Siberian NC_000018.9 - 51024516 Apr 27, 2020 (154)
91 8.3KJPN NC_000018.9 - 51024516 Apr 27, 2021 (155)
92 TopMed NC_000018.10 - 53498146 Apr 27, 2021 (155)
93 UK 10K study - Twins NC_000018.9 - 51024516 Oct 12, 2018 (152)
94 A Vietnamese Genetic Variation Database NC_000018.9 - 51024516 Jul 13, 2019 (153)
95 ALFA NC_000018.10 - 53498146 Apr 27, 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
ss110568787, ss160363365, ss255678890, ss283006047, ss287289156, ss480004849, ss1697832461, ss1713629287, ss3643174043 NC_000018.8:49278513:T:C NC_000018.10:53498145:T:C (self)
74529751, 41299271, 29177244, 4612738, 18398119, 44165077, 15864405, 19280951, 39123203, 10412714, 83330544, 41299271, 9125130, ss227881962, ss237482352, ss243728956, ss480013548, ss480671076, ss484800513, ss536883222, ss565666129, ss661500330, ss778435563, ss782846890, ss783811485, ss832100705, ss833891061, ss993771351, ss1081532149, ss1361194898, ss1428230250, ss1578421446, ss1636967255, ss1679961288, ss1752259738, ss1937239029, ss1968533639, ss2029389325, ss2157896360, ss2387323785, ss2629192628, ss2633478187, ss2702486493, ss2957162451, ss3016594611, ss3352042406, ss3627818766, ss3631454583, ss3633164084, ss3633872929, ss3634707921, ss3635560178, ss3636397309, ss3637311795, ss3638198497, ss3640415229, ss3683438996, ss3742579540, ss3745008064, ss3755443218, ss3772505537, ss3835190345, ss3887106223, ss3936987683, ss4017800385, ss5225361237 NC_000018.9:51024515:T:C NC_000018.10:53498145:T:C (self)
525756932, 1610737, 36606196, 170789652, 273739093, 4615276387, ss2221924290, ss3028523829, ss3280393415, ss3701742813, ss3820700214, ss3980228195, ss5058193430 NC_000018.10:53498145:T:C NC_000018.10:53498145:T:C (self)
ss14411807 NT_010966.13:32513617:T:C NC_000018.10:53498145:T:C (self)
ss2333105, ss24090954, ss65789682, ss74855133, ss106547125, ss119395711, ss172544893 NT_010966.14:32513617:T:C NC_000018.10:53498145: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 rs1502223

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