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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.

rs874515

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:23552468 (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
G>A / G>C
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.254645 (67402/264690, TOPMED)
C=0.246534 (34534/140078, GnomAD)
G=0.42088 (7054/16760, 8.3KJPN) (+ 15 more)
C=0.17248 (2800/16234, ALFA)
C=0.2859 (1432/5008, 1000G)
C=0.2636 (1181/4480, Estonian)
C=0.2748 (1059/3854, ALSPAC)
C=0.2826 (1048/3708, TWINSUK)
G=0.4273 (1252/2930, KOREAN)
G=0.4230 (775/1832, Korea1K)
C=0.285 (284/998, GoNL)
C=0.247 (148/600, NorthernSweden)
C=0.296 (97/328, HapMap)
G=0.359 (102/284, SGDP_PRJ)
C=0.333 (72/216, Qatari)
C=0.495 (104/210, Vietnamese)
C=0.28 (11/40, GENOME_DK)
G=0.42 (11/26, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
LOC105376859 : 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.23552468G>A
GRCh38.p13 chr 1 NC_000001.11:g.23552468G>C
GRCh37.p13 chr 1 NC_000001.10:g.23878959G>A
GRCh37.p13 chr 1 NC_000001.10:g.23878959G>C
chr 1 novel patch HSCHR1_4_CTG3 NW_014040926.1:g.322447G>A
chr 1 novel patch HSCHR1_4_CTG3 NW_014040926.1:g.322447G>C
Gene: LOC105376859, uncharacterized LOC105376859 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
LOC105376859 transcript variant X1 XR_947064.3:n. N/A Intron Variant
LOC105376859 transcript variant X2 XR_947065.3:n. 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 16234 G=0.82752 A=0.00000, C=0.17248
European Sub 12848 G=0.79281 A=0.00000, C=0.20719
African Sub 2416 G=0.9764 A=0.0000, C=0.0236
African Others Sub 100 G=0.98 A=0.00, C=0.02
African American Sub 2316 G=0.9763 A=0.0000, C=0.0237
Asian Sub 36 G=0.92 A=0.00, C=0.08
East Asian Sub 28 G=0.93 A=0.00, C=0.07
Other Asian Sub 8 G=0.9 A=0.0, C=0.1
Latin American 1 Sub 70 G=1.00 A=0.00, C=0.00
Latin American 2 Sub 280 G=1.000 A=0.000, C=0.000
South Asian Sub 58 G=0.98 A=0.00, C=0.02
Other Sub 526 G=0.854 A=0.000, C=0.146


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").

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Study Population Group Sample Size Ref Allele Alt Allele
TopMed Global Study-wide 264690 G=0.745355 C=0.254645
gnomAD - Genomes Global Study-wide 140078 G=0.753466 C=0.246534
gnomAD - Genomes European Sub 75850 G=0.71230 C=0.28770
gnomAD - Genomes African Sub 42006 G=0.88275 C=0.11725
gnomAD - Genomes American Sub 13636 G=0.70424 C=0.29576
gnomAD - Genomes Ashkenazi Jewish Sub 3320 G=0.5708 C=0.4292
gnomAD - Genomes East Asian Sub 3114 G=0.4563 C=0.5437
gnomAD - Genomes Other Sub 2152 G=0.7045 C=0.2955
8.3KJPN JAPANESE Study-wide 16760 G=0.42088 C=0.57912
Allele Frequency Aggregator Total Global 16234 G=0.82752 A=0.00000, C=0.17248
Allele Frequency Aggregator European Sub 12848 G=0.79281 A=0.00000, C=0.20719
Allele Frequency Aggregator African Sub 2416 G=0.9764 A=0.0000, C=0.0236
Allele Frequency Aggregator Other Sub 526 G=0.854 A=0.000, C=0.146
Allele Frequency Aggregator Latin American 2 Sub 280 G=1.000 A=0.000, C=0.000
Allele Frequency Aggregator Latin American 1 Sub 70 G=1.00 A=0.00, C=0.00
Allele Frequency Aggregator South Asian Sub 58 G=0.98 A=0.00, C=0.02
Allele Frequency Aggregator Asian Sub 36 G=0.92 A=0.00, C=0.08
1000Genomes Global Study-wide 5008 G=0.7141 C=0.2859
1000Genomes African Sub 1322 G=0.9130 C=0.0870
1000Genomes East Asian Sub 1008 G=0.4474 C=0.5526
1000Genomes Europe Sub 1006 G=0.7028 C=0.2972
1000Genomes South Asian Sub 978 G=0.763 C=0.237
1000Genomes American Sub 694 G=0.670 C=0.330
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.7364 C=0.2636
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.7252 C=0.2748
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.7174 C=0.2826
KOREAN population from KRGDB KOREAN Study-wide 2930 G=0.4273 C=0.5727
Korean Genome Project KOREAN Study-wide 1832 G=0.4230 C=0.5770
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.715 C=0.285
Northern Sweden ACPOP Study-wide 600 G=0.753 C=0.247
HapMap Global Study-wide 328 G=0.704 C=0.296
HapMap African Sub 120 G=0.917 C=0.083
HapMap American Sub 120 G=0.783 C=0.217
HapMap Asian Sub 88 G=0.31 C=0.69
SGDP_PRJ Global Study-wide 284 G=0.359 C=0.641
Qatari Global Study-wide 216 G=0.667 C=0.333
A Vietnamese Genetic Variation Database Global Study-wide 210 G=0.505 C=0.495
The Danish reference pan genome Danish Study-wide 40 G=0.72 C=0.28
Siberian Global Study-wide 26 G=0.42 C=0.58
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
GRCh38.p13 chr 1 NC_000001.11:g.23552468= NC_000001.11:g.23552468G>A NC_000001.11:g.23552468G>C
GRCh37.p13 chr 1 NC_000001.10:g.23878959= NC_000001.10:g.23878959G>A NC_000001.10:g.23878959G>C
chr 1 novel patch HSCHR1_4_CTG3 NW_014040926.1:g.322447= NW_014040926.1:g.322447G>A NW_014040926.1:g.322447G>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#.

58 SubSNP, 18 Frequency submissions
No Submitter Submission ID Date (Build)
1 TSC-CSHL ss1298676 Oct 05, 2000 (86)
2 ABI ss43838122 Mar 15, 2006 (126)
3 ILLUMINA ss65720419 Oct 15, 2006 (127)
4 BCMHGSC_JDW ss87299506 Mar 23, 2008 (129)
5 HUMANGENOME_JCVI ss99194171 Feb 05, 2009 (130)
6 BGI ss102727785 Dec 01, 2009 (131)
7 ILLUMINA ss120244567 Dec 01, 2009 (131)
8 ENSEMBL ss137845191 Dec 01, 2009 (131)
9 GMI ss154769402 Dec 01, 2009 (131)
10 COMPLETE_GENOMICS ss163978523 Jul 04, 2010 (132)
11 COMPLETE_GENOMICS ss166240138 Jul 04, 2010 (132)
12 ILLUMINA ss174759403 Jul 04, 2010 (132)
13 BUSHMAN ss198168580 Jul 04, 2010 (132)
14 1000GENOMES ss218283621 Jul 14, 2010 (132)
15 1000GENOMES ss230462767 Jul 14, 2010 (132)
16 1000GENOMES ss238170316 Jul 15, 2010 (132)
17 GMI ss275753365 May 04, 2012 (137)
18 TISHKOFF ss553892982 Apr 25, 2013 (138)
19 SSMP ss647640297 Apr 25, 2013 (138)
20 EVA-GONL ss974948056 Aug 21, 2014 (142)
21 JMKIDD_LAB ss1067735817 Aug 21, 2014 (142)
22 1000GENOMES ss1290042221 Aug 21, 2014 (142)
23 DDI ss1425745882 Apr 01, 2015 (144)
24 EVA_GENOME_DK ss1573942312 Apr 01, 2015 (144)
25 EVA_DECODE ss1584306328 Apr 01, 2015 (144)
26 EVA_UK10K_ALSPAC ss1599730184 Apr 01, 2015 (144)
27 EVA_UK10K_TWINSUK ss1642724217 Apr 01, 2015 (144)
28 HAMMER_LAB ss1794065634 Sep 08, 2015 (146)
29 WEILL_CORNELL_DGM ss1918159710 Feb 12, 2016 (147)
30 GENOMED ss1966705300 Jul 19, 2016 (147)
31 JJLAB ss2019591934 Sep 14, 2016 (149)
32 USC_VALOUEV ss2147597004 Dec 20, 2016 (150)
33 HUMAN_LONGEVITY ss2160735307 Dec 20, 2016 (150)
34 TOPMED ss2322925323 Dec 20, 2016 (150)
35 SYSTEMSBIOZJU ss2624312415 Nov 08, 2017 (151)
36 GRF ss2697502158 Nov 08, 2017 (151)
37 GNOMAD ss2752684021 Nov 08, 2017 (151)
38 SWEGEN ss2986468463 Nov 08, 2017 (151)
39 BIOINF_KMB_FNS_UNIBA ss3023561413 Nov 08, 2017 (151)
40 TOPMED ss3070964531 Nov 08, 2017 (151)
41 CSHL ss3343368062 Nov 08, 2017 (151)
42 ILLUMINA ss3637743138 Oct 11, 2018 (152)
43 URBANLAB ss3646622811 Oct 11, 2018 (152)
44 EGCUT_WGS ss3654536644 Jul 12, 2019 (153)
45 EVA_DECODE ss3686349000 Jul 12, 2019 (153)
46 ACPOP ss3726870688 Jul 12, 2019 (153)
47 EVA ss3745942977 Jul 12, 2019 (153)
48 PACBIO ss3783353790 Jul 12, 2019 (153)
49 PACBIO ss3789023287 Jul 12, 2019 (153)
50 PACBIO ss3793895792 Jul 12, 2019 (153)
51 KHV_HUMAN_GENOMES ss3798962077 Jul 12, 2019 (153)
52 EVA ss3826072042 Apr 25, 2020 (154)
53 SGDP_PRJ ss3848409341 Apr 25, 2020 (154)
54 KRGDB ss3893326289 Apr 25, 2020 (154)
55 KOGIC ss3944037903 Apr 25, 2020 (154)
56 EVA ss4016898333 Apr 25, 2021 (155)
57 TOPMED ss4442184469 Apr 25, 2021 (155)
58 TOMMO_GENOMICS ss5142936665 Apr 25, 2021 (155)
59 1000Genomes NC_000001.10 - 23878959 Oct 11, 2018 (152)
60 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 23878959 Oct 11, 2018 (152)
61 Genetic variation in the Estonian population NC_000001.10 - 23878959 Oct 11, 2018 (152)
62 The Danish reference pan genome NC_000001.10 - 23878959 Apr 25, 2020 (154)
63 gnomAD - Genomes NC_000001.11 - 23552468 Apr 25, 2021 (155)
64 Genome of the Netherlands Release 5 NC_000001.10 - 23878959 Apr 25, 2020 (154)
65 HapMap NC_000001.11 - 23552468 Apr 25, 2020 (154)
66 KOREAN population from KRGDB NC_000001.10 - 23878959 Apr 25, 2020 (154)
67 Korean Genome Project NC_000001.11 - 23552468 Apr 25, 2020 (154)
68 Northern Sweden NC_000001.10 - 23878959 Jul 12, 2019 (153)
69 Qatari NC_000001.10 - 23878959 Apr 25, 2020 (154)
70 SGDP_PRJ NC_000001.10 - 23878959 Apr 25, 2020 (154)
71 Siberian NC_000001.10 - 23878959 Apr 25, 2020 (154)
72 8.3KJPN NC_000001.10 - 23878959 Apr 25, 2021 (155)
73 TopMed NC_000001.11 - 23552468 Apr 25, 2021 (155)
74 UK 10K study - Twins NC_000001.10 - 23878959 Oct 11, 2018 (152)
75 A Vietnamese Genetic Variation Database NC_000001.10 - 23878959 Jul 12, 2019 (153)
76 ALFA NC_000001.11 - 23552468 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
872614621 NC_000001.11:23552467:G:A NC_000001.11:23552467:G:A
ss87299506, ss163978523, ss166240138, ss198168580, ss275753365, ss1584306328 NC_000001.9:23751545:G:C NC_000001.11:23552467:G:C (self)
730548, 387531, 274892, 1426465, 168238, 503683, 155553, 201640, 426321, 113358, 905972, 387531, 82077, ss218283621, ss230462767, ss238170316, ss553892982, ss647640297, ss974948056, ss1067735817, ss1290042221, ss1425745882, ss1573942312, ss1599730184, ss1642724217, ss1794065634, ss1918159710, ss1966705300, ss2019591934, ss2147597004, ss2322925323, ss2624312415, ss2697502158, ss2752684021, ss2986468463, ss3343368062, ss3637743138, ss3654536644, ss3726870688, ss3745942977, ss3783353790, ss3789023287, ss3793895792, ss3826072042, ss3848409341, ss3893326289, ss4016898333, ss5142936665 NC_000001.10:23878958:G:C NC_000001.11:23552467:G:C (self)
5083641, 30559, 415904, 3641391, 5790804, 872614621, ss2160735307, ss3023561413, ss3070964531, ss3646622811, ss3686349000, ss3798962077, ss3944037903, ss4442184469 NC_000001.11:23552467:G:C NC_000001.11:23552467:G:C (self)
ss1298676, ss43838122, ss65720419, ss99194171, ss102727785, ss120244567, ss137845191, ss154769402, ss174759403 NT_004610.19:10559046:G:C NC_000001.11:23552467:G: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 rs874515

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