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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.

rs262045

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr5:178581826 (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>G / C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.394182 (104336/264690, TOPMED)
C=0.425632 (59523/139846, GnomAD)
C=0.25352 (7164/28258, 14KJPN) (+ 17 more)
C=0.49811 (8939/17946, ALFA)
C=0.25656 (4300/16760, 8.3KJPN)
C=0.3184 (2039/6404, 1000G_30x)
C=0.3215 (1610/5008, 1000G)
G=0.4491 (2012/4480, Estonian)
G=0.4001 (1542/3854, ALSPAC)
G=0.4010 (1487/3708, TWINSUK)
C=0.2474 (725/2930, KOREAN)
C=0.2850 (538/1888, HapMap)
C=0.2495 (457/1832, Korea1K)
G=0.397 (396/998, GoNL)
G=0.377 (226/600, NorthernSweden)
C=0.206 (97/470, SGDP_PRJ)
C=0.264 (57/216, Qatari)
C=0.297 (63/212, Vietnamese)
C=0.42 (20/48, Siberian)
G=0.38 (15/40, GENOME_DK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
COL23A1 : 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 17946 C=0.49811 G=0.50189, T=0.00000
European Sub 13854 C=0.57269 G=0.42731, T=0.00000
African Sub 2438 C=0.1473 G=0.8527, T=0.0000
African Others Sub 90 C=0.04 G=0.96, T=0.00
African American Sub 2348 C=0.1512 G=0.8488, T=0.0000
Asian Sub 112 C=0.241 G=0.759, T=0.000
East Asian Sub 86 C=0.24 G=0.76, T=0.00
Other Asian Sub 26 C=0.23 G=0.77, T=0.00
Latin American 1 Sub 146 C=0.342 G=0.658, T=0.000
Latin American 2 Sub 610 C=0.403 G=0.597, T=0.000
South Asian Sub 98 C=0.38 G=0.62, T=0.00
Other Sub 688 C=0.416 G=0.584, 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 C=0.394182 G=0.605818
gnomAD - Genomes Global Study-wide 139846 C=0.425632 G=0.574368
gnomAD - Genomes European Sub 75728 C=0.58570 G=0.41430
gnomAD - Genomes African Sub 41936 C=0.14472 G=0.85528
gnomAD - Genomes American Sub 13606 C=0.41371 G=0.58629
gnomAD - Genomes Ashkenazi Jewish Sub 3314 C=0.5160 G=0.4840
gnomAD - Genomes East Asian Sub 3116 C=0.2628 G=0.7372
gnomAD - Genomes Other Sub 2146 C=0.4390 G=0.5610
14KJPN JAPANESE Study-wide 28258 C=0.25352 G=0.74648
Allele Frequency Aggregator Total Global 17946 C=0.49811 G=0.50189, T=0.00000
Allele Frequency Aggregator European Sub 13854 C=0.57269 G=0.42731, T=0.00000
Allele Frequency Aggregator African Sub 2438 C=0.1473 G=0.8527, T=0.0000
Allele Frequency Aggregator Other Sub 688 C=0.416 G=0.584, T=0.000
Allele Frequency Aggregator Latin American 2 Sub 610 C=0.403 G=0.597, T=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 C=0.342 G=0.658, T=0.000
Allele Frequency Aggregator Asian Sub 112 C=0.241 G=0.759, T=0.000
Allele Frequency Aggregator South Asian Sub 98 C=0.38 G=0.62, T=0.00
8.3KJPN JAPANESE Study-wide 16760 C=0.25656 G=0.74344
1000Genomes_30x Global Study-wide 6404 C=0.3184 G=0.6816
1000Genomes_30x African Sub 1786 C=0.0622 G=0.9378
1000Genomes_30x Europe Sub 1266 C=0.5885 G=0.4115
1000Genomes_30x South Asian Sub 1202 C=0.3702 G=0.6298
1000Genomes_30x East Asian Sub 1170 C=0.2726 G=0.7274
1000Genomes_30x American Sub 980 C=0.428 G=0.572
1000Genomes Global Study-wide 5008 C=0.3215 G=0.6785
1000Genomes African Sub 1322 C=0.0635 G=0.9365
1000Genomes East Asian Sub 1008 C=0.2768 G=0.7232
1000Genomes Europe Sub 1006 C=0.5895 G=0.4105
1000Genomes South Asian Sub 978 C=0.374 G=0.626
1000Genomes American Sub 694 C=0.415 G=0.585
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.5509 G=0.4491
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.5999 G=0.4001
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.5990 G=0.4010
KOREAN population from KRGDB KOREAN Study-wide 2930 C=0.2474 G=0.7526, T=0.0000
HapMap Global Study-wide 1888 C=0.2850 G=0.7150
HapMap American Sub 768 C=0.401 G=0.599
HapMap African Sub 690 C=0.083 G=0.917
HapMap Asian Sub 254 C=0.303 G=0.697
HapMap Europe Sub 176 C=0.545 G=0.455
Korean Genome Project KOREAN Study-wide 1832 C=0.2495 G=0.7505
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 C=0.603 G=0.397
Northern Sweden ACPOP Study-wide 600 C=0.623 G=0.377
SGDP_PRJ Global Study-wide 470 C=0.206 G=0.794
Qatari Global Study-wide 216 C=0.264 G=0.736
A Vietnamese Genetic Variation Database Global Study-wide 212 C=0.297 G=0.703
Siberian Global Study-wide 48 C=0.42 G=0.58
The Danish reference pan genome Danish Study-wide 40 C=0.62 G=0.38
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 5 NC_000005.10:g.178581826C>G
GRCh38.p14 chr 5 NC_000005.10:g.178581826C>T
GRCh37.p13 chr 5 NC_000005.9:g.178008827C>G
GRCh37.p13 chr 5 NC_000005.9:g.178008827C>T
Gene: COL23A1, collagen type XXIII alpha 1 chain (minus strand)
Molecule type Change Amino acid[Codon] SO Term
COL23A1 transcript NM_173465.4:c.294+8078G>C N/A Intron Variant
COL23A1 transcript variant X1 XM_006714933.4:c.294+8078…

XM_006714933.4:c.294+8078G>C

N/A Intron Variant
COL23A1 transcript variant X3 XM_006714934.4:c.294+8078…

XM_006714934.4:c.294+8078G>C

N/A Intron Variant
COL23A1 transcript variant X4 XM_006714935.4:c.294+8078…

XM_006714935.4:c.294+8078G>C

N/A Intron Variant
COL23A1 transcript variant X6 XM_006714936.4:c.294+8078…

XM_006714936.4:c.294+8078G>C

N/A Intron Variant
COL23A1 transcript variant X2 XM_011534688.3:c.294+8078…

XM_011534688.3:c.294+8078G>C

N/A Intron Variant
COL23A1 transcript variant X5 XM_011534690.3:c.294+8078…

XM_011534690.3:c.294+8078G>C

N/A Intron Variant
COL23A1 transcript variant X7 XM_011534691.3:c.294+8078…

XM_011534691.3:c.294+8078G>C

N/A Intron Variant
COL23A1 transcript variant X10 XM_017010018.2:c.294+8078…

XM_017010018.2:c.294+8078G>C

N/A Intron Variant
COL23A1 transcript variant X8 XM_047417869.1:c.294+8078…

XM_047417869.1:c.294+8078G>C

N/A Intron Variant
COL23A1 transcript variant X9 XM_011534692.3:c. N/A Genic Upstream Transcript 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= G T
GRCh38.p14 chr 5 NC_000005.10:g.178581826= NC_000005.10:g.178581826C>G NC_000005.10:g.178581826C>T
GRCh37.p13 chr 5 NC_000005.9:g.178008827= NC_000005.9:g.178008827C>G NC_000005.9:g.178008827C>T
COL23A1 transcript NM_173465.3:c.294+8078= NM_173465.3:c.294+8078G>C NM_173465.3:c.294+8078G>A
COL23A1 transcript NM_173465.4:c.294+8078= NM_173465.4:c.294+8078G>C NM_173465.4:c.294+8078G>A
COL23A1 transcript variant X1 XM_005266009.1:c.294+8078= XM_005266009.1:c.294+8078G>C XM_005266009.1:c.294+8078G>A
COL23A1 transcript variant X1 XM_006714933.4:c.294+8078= XM_006714933.4:c.294+8078G>C XM_006714933.4:c.294+8078G>A
COL23A1 transcript variant X3 XM_006714934.4:c.294+8078= XM_006714934.4:c.294+8078G>C XM_006714934.4:c.294+8078G>A
COL23A1 transcript variant X4 XM_006714935.4:c.294+8078= XM_006714935.4:c.294+8078G>C XM_006714935.4:c.294+8078G>A
COL23A1 transcript variant X6 XM_006714936.4:c.294+8078= XM_006714936.4:c.294+8078G>C XM_006714936.4:c.294+8078G>A
COL23A1 transcript variant X2 XM_011534688.3:c.294+8078= XM_011534688.3:c.294+8078G>C XM_011534688.3:c.294+8078G>A
COL23A1 transcript variant X5 XM_011534690.3:c.294+8078= XM_011534690.3:c.294+8078G>C XM_011534690.3:c.294+8078G>A
COL23A1 transcript variant X7 XM_011534691.3:c.294+8078= XM_011534691.3:c.294+8078G>C XM_011534691.3:c.294+8078G>A
COL23A1 transcript variant X10 XM_017010018.2:c.294+8078= XM_017010018.2:c.294+8078G>C XM_017010018.2:c.294+8078G>A
COL23A1 transcript variant X8 XM_047417869.1:c.294+8078= XM_047417869.1:c.294+8078G>C XM_047417869.1:c.294+8078G>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#.

75 SubSNP, 20 Frequency submissions
No Submitter Submission ID Date (Build)
1 KWOK ss342034 Jul 12, 2000 (79)
2 KWOK ss898358 Oct 04, 2000 (86)
3 KWOK ss899055 Oct 04, 2000 (86)
4 SC_JCM ss4128887 Nov 05, 2001 (101)
5 WI_SSAHASNP ss14653518 Dec 05, 2003 (119)
6 CSHL-HAPMAP ss19611776 Feb 27, 2004 (120)
7 SSAHASNP ss22244742 Apr 05, 2004 (121)
8 ABI ss44586655 Mar 14, 2006 (126)
9 AFFY ss76569102 Dec 06, 2007 (129)
10 HUMANGENOME_JCVI ss98792172 Feb 05, 2009 (130)
11 KRIBB_YJKIM ss104812996 Feb 05, 2009 (130)
12 BGI ss105972555 Feb 05, 2009 (130)
13 1000GENOMES ss109664299 Jan 24, 2009 (130)
14 1000GENOMES ss113739020 Jan 25, 2009 (130)
15 ILLUMINA-UK ss116926001 Feb 14, 2009 (130)
16 GMI ss156395729 Dec 01, 2009 (131)
17 COMPLETE_GENOMICS ss162936932 Jul 04, 2010 (132)
18 COMPLETE_GENOMICS ss166353459 Jul 04, 2010 (132)
19 COMPLETE_GENOMICS ss167412045 Jul 04, 2010 (132)
20 BUSHMAN ss201274224 Jul 04, 2010 (132)
21 BCM-HGSC-SUB ss206860148 Jul 04, 2010 (132)
22 1000GENOMES ss222145909 Jul 14, 2010 (132)
23 1000GENOMES ss233277318 Jul 14, 2010 (132)
24 1000GENOMES ss240373091 Jul 15, 2010 (132)
25 BL ss253965815 May 09, 2011 (134)
26 GMI ss278607631 May 04, 2012 (137)
27 GMI ss285318397 Apr 25, 2013 (138)
28 PJP ss293530955 May 09, 2011 (134)
29 TISHKOFF ss558925672 Apr 25, 2013 (138)
30 SSMP ss652837097 Apr 25, 2013 (138)
31 EVA-GONL ss982467742 Aug 21, 2014 (142)
32 JMKIDD_LAB ss1073296379 Aug 21, 2014 (142)
33 1000GENOMES ss1318542273 Aug 21, 2014 (142)
34 DDI ss1430600518 Apr 01, 2015 (144)
35 EVA_GENOME_DK ss1581484924 Apr 01, 2015 (144)
36 EVA_DECODE ss1592011694 Apr 01, 2015 (144)
37 EVA_UK10K_ALSPAC ss1614722120 Apr 01, 2015 (144)
38 EVA_UK10K_TWINSUK ss1657716153 Apr 01, 2015 (144)
39 EVA_SVP ss1712826384 Apr 01, 2015 (144)
40 HAMMER_LAB ss1804226360 Sep 08, 2015 (146)
41 WEILL_CORNELL_DGM ss1925722072 Feb 12, 2016 (147)
42 GENOMED ss1970283593 Jul 19, 2016 (147)
43 JJLAB ss2023474739 Sep 14, 2016 (149)
44 USC_VALOUEV ss2151634681 Dec 20, 2016 (150)
45 HUMAN_LONGEVITY ss2280916434 Dec 20, 2016 (150)
46 SYSTEMSBIOZJU ss2626225394 Nov 08, 2017 (151)
47 GRF ss2707216236 Nov 08, 2017 (151)
48 GNOMAD ss2834585964 Nov 08, 2017 (151)
49 SWEGEN ss2998333745 Nov 08, 2017 (151)
50 BIOINF_KMB_FNS_UNIBA ss3025519505 Nov 08, 2017 (151)
51 CSHL ss3346779650 Nov 08, 2017 (151)
52 URBANLAB ss3648240711 Oct 12, 2018 (152)
53 EGCUT_WGS ss3666260270 Jul 13, 2019 (153)
54 EVA_DECODE ss3716361134 Jul 13, 2019 (153)
55 ACPOP ss3733104085 Jul 13, 2019 (153)
56 EVA ss3764474408 Jul 13, 2019 (153)
57 KHV_HUMAN_GENOMES ss3807636076 Jul 13, 2019 (153)
58 EVA ss3829670918 Apr 26, 2020 (154)
59 EVA ss3838309394 Apr 26, 2020 (154)
60 SGDP_PRJ ss3863679038 Apr 26, 2020 (154)
61 KRGDB ss3910402778 Apr 26, 2020 (154)
62 KOGIC ss3958281568 Apr 26, 2020 (154)
63 TOPMED ss4690190583 Apr 26, 2021 (155)
64 TOMMO_GENOMICS ss5175663604 Apr 26, 2021 (155)
65 1000G_HIGH_COVERAGE ss5267015801 Oct 13, 2022 (156)
66 EVA ss5363117202 Oct 13, 2022 (156)
67 HUGCELL_USP ss5464851966 Oct 13, 2022 (156)
68 1000G_HIGH_COVERAGE ss5552263216 Oct 13, 2022 (156)
69 SANFORD_IMAGENETICS ss5639546492 Oct 13, 2022 (156)
70 TOMMO_GENOMICS ss5713182455 Oct 13, 2022 (156)
71 YY_MCH ss5807052740 Oct 13, 2022 (156)
72 EVA ss5836099128 Oct 13, 2022 (156)
73 EVA ss5855153344 Oct 13, 2022 (156)
74 EVA ss5897666393 Oct 13, 2022 (156)
75 EVA ss5968040124 Oct 13, 2022 (156)
76 1000Genomes NC_000005.9 - 178008827 Oct 12, 2018 (152)
77 1000Genomes_30x NC_000005.10 - 178581826 Oct 13, 2022 (156)
78 The Avon Longitudinal Study of Parents and Children NC_000005.9 - 178008827 Oct 12, 2018 (152)
79 Genetic variation in the Estonian population NC_000005.9 - 178008827 Oct 12, 2018 (152)
80 The Danish reference pan genome NC_000005.9 - 178008827 Apr 26, 2020 (154)
81 gnomAD - Genomes NC_000005.10 - 178581826 Apr 26, 2021 (155)
82 Genome of the Netherlands Release 5 NC_000005.9 - 178008827 Apr 26, 2020 (154)
83 HapMap NC_000005.10 - 178581826 Apr 26, 2020 (154)
84 KOREAN population from KRGDB NC_000005.9 - 178008827 Apr 26, 2020 (154)
85 Korean Genome Project NC_000005.10 - 178581826 Apr 26, 2020 (154)
86 Northern Sweden NC_000005.9 - 178008827 Jul 13, 2019 (153)
87 Qatari NC_000005.9 - 178008827 Apr 26, 2020 (154)
88 SGDP_PRJ NC_000005.9 - 178008827 Apr 26, 2020 (154)
89 Siberian NC_000005.9 - 178008827 Apr 26, 2020 (154)
90 8.3KJPN NC_000005.9 - 178008827 Apr 26, 2021 (155)
91 14KJPN NC_000005.10 - 178581826 Oct 13, 2022 (156)
92 TopMed NC_000005.10 - 178581826 Apr 26, 2021 (155)
93 UK 10K study - Twins NC_000005.9 - 178008827 Oct 12, 2018 (152)
94 A Vietnamese Genetic Variation Database NC_000005.9 - 178008827 Jul 13, 2019 (153)
95 ALFA NC_000005.10 - 178581826 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
ss76569102, ss109664299, ss113739020, ss116926001, ss162936932, ss166353459, ss167412045, ss201274224, ss206860148, ss253965815, ss278607631, ss285318397, ss293530955, ss1592011694, ss1712826384 NC_000005.8:177941432:C:G NC_000005.10:178581825:C:G (self)
30268046, 16849830, 11998518, 7649863, 7477200, 17580172, 6388950, 7764002, 15696018, 4151035, 33632911, 16849830, 3731787, ss222145909, ss233277318, ss240373091, ss558925672, ss652837097, ss982467742, ss1073296379, ss1318542273, ss1430600518, ss1581484924, ss1614722120, ss1657716153, ss1804226360, ss1925722072, ss1970283593, ss2023474739, ss2151634681, ss2626225394, ss2707216236, ss2834585964, ss2998333745, ss3346779650, ss3666260270, ss3733104085, ss3764474408, ss3829670918, ss3838309394, ss3863679038, ss3910402778, ss5175663604, ss5363117202, ss5639546492, ss5836099128, ss5968040124 NC_000005.9:178008826:C:G NC_000005.10:178581825:C:G (self)
39789151, 214072694, 3036773, 14659569, 47019559, 527568140, 4195120390, ss2280916434, ss3025519505, ss3648240711, ss3716361134, ss3807636076, ss3958281568, ss4690190583, ss5267015801, ss5464851966, ss5552263216, ss5713182455, ss5807052740, ss5855153344, ss5897666393 NC_000005.10:178581825:C:G NC_000005.10:178581825:C:G (self)
ss342034, ss898358, ss899055, ss4128887, ss44586655, ss98792172, ss104812996, ss105972555, ss156395729 NT_023133.13:22820099:C:G NC_000005.10:178581825:C:G (self)
ss14653518, ss19611776, ss22244742 NT_077451.3:1104032:C:G NC_000005.10:178581825:C:G (self)
17580172, ss3910402778 NC_000005.9:178008826:C:T NC_000005.10:178581825:C:T (self)
4195120390 NC_000005.10:178581825:C:T NC_000005.10:178581825: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.

No publications for rs262045

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