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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.

rs12454530

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr18:56039476 (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
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.232600 (61567/264690, TOPMED)
A=0.229026 (32071/140032, GnomAD)
A=0.08872 (2507/28258, 14KJPN) (+ 18 more)
A=0.27714 (6642/23966, ALFA)
A=0.08675 (1454/16760, 8.3KJPN)
A=0.2355 (1508/6404, 1000G_30x)
A=0.2342 (1173/5008, 1000G)
A=0.3049 (1366/4480, Estonian)
A=0.2999 (1156/3854, ALSPAC)
A=0.2994 (1110/3708, TWINSUK)
A=0.1129 (330/2922, KOREAN)
A=0.1608 (304/1890, HapMap)
A=0.1135 (208/1832, Korea1K)
A=0.322 (321/998, GoNL)
A=0.425 (266/626, Chileans)
A=0.265 (159/600, NorthernSweden)
G=0.374 (89/238, SGDP_PRJ)
A=0.264 (57/216, Qatari)
A=0.198 (42/212, Vietnamese)
A=0.40 (16/40, GENOME_DK)
G=0.43 (12/28, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
LOC642484 : 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 23966 G=0.72286 A=0.27714
European Sub 15664 G=0.70735 A=0.29265
African Sub 3624 G=0.9194 A=0.0806
African Others Sub 126 G=0.976 A=0.024
African American Sub 3498 G=0.9174 A=0.0826
Asian Sub 160 G=0.863 A=0.138
East Asian Sub 102 G=0.853 A=0.147
Other Asian Sub 58 G=0.88 A=0.12
Latin American 1 Sub 292 G=0.637 A=0.363
Latin American 2 Sub 2770 G=0.5715 A=0.4285
South Asian Sub 110 G=0.645 A=0.355
Other Sub 1346 G=0.6939 A=0.3061


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=0.767400 A=0.232600
gnomAD - Genomes Global Study-wide 140032 G=0.770974 A=0.229026
gnomAD - Genomes European Sub 75818 G=0.71347 A=0.28653
gnomAD - Genomes African Sub 41988 G=0.90797 A=0.09203
gnomAD - Genomes American Sub 13630 G=0.66398 A=0.33602
gnomAD - Genomes Ashkenazi Jewish Sub 3322 G=0.6905 A=0.3095
gnomAD - Genomes East Asian Sub 3128 G=0.8923 A=0.1077
gnomAD - Genomes Other Sub 2146 G=0.7493 A=0.2507
14KJPN JAPANESE Study-wide 28258 G=0.91128 A=0.08872
Allele Frequency Aggregator Total Global 23966 G=0.72286 A=0.27714
Allele Frequency Aggregator European Sub 15664 G=0.70735 A=0.29265
Allele Frequency Aggregator African Sub 3624 G=0.9194 A=0.0806
Allele Frequency Aggregator Latin American 2 Sub 2770 G=0.5715 A=0.4285
Allele Frequency Aggregator Other Sub 1346 G=0.6939 A=0.3061
Allele Frequency Aggregator Latin American 1 Sub 292 G=0.637 A=0.363
Allele Frequency Aggregator Asian Sub 160 G=0.863 A=0.138
Allele Frequency Aggregator South Asian Sub 110 G=0.645 A=0.355
8.3KJPN JAPANESE Study-wide 16760 G=0.91325 A=0.08675
1000Genomes_30x Global Study-wide 6404 G=0.7645 A=0.2355
1000Genomes_30x African Sub 1786 G=0.9490 A=0.0510
1000Genomes_30x Europe Sub 1266 G=0.7164 A=0.2836
1000Genomes_30x South Asian Sub 1202 G=0.5715 A=0.4285
1000Genomes_30x East Asian Sub 1170 G=0.8496 A=0.1504
1000Genomes_30x American Sub 980 G=0.626 A=0.374
1000Genomes Global Study-wide 5008 G=0.7658 A=0.2342
1000Genomes African Sub 1322 G=0.9463 A=0.0537
1000Genomes East Asian Sub 1008 G=0.8472 A=0.1528
1000Genomes Europe Sub 1006 G=0.7187 A=0.2813
1000Genomes South Asian Sub 978 G=0.580 A=0.420
1000Genomes American Sub 694 G=0.634 A=0.366
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.6951 A=0.3049
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.7001 A=0.2999
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.7006 A=0.2994
KOREAN population from KRGDB KOREAN Study-wide 2922 G=0.8871 A=0.1129
HapMap Global Study-wide 1890 G=0.8392 A=0.1608
HapMap American Sub 770 G=0.745 A=0.255
HapMap African Sub 690 G=0.954 A=0.046
HapMap Asian Sub 254 G=0.882 A=0.118
HapMap Europe Sub 176 G=0.739 A=0.261
Korean Genome Project KOREAN Study-wide 1832 G=0.8865 A=0.1135
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.678 A=0.322
Chileans Chilean Study-wide 626 G=0.575 A=0.425
Northern Sweden ACPOP Study-wide 600 G=0.735 A=0.265
SGDP_PRJ Global Study-wide 238 G=0.374 A=0.626
Qatari Global Study-wide 216 G=0.736 A=0.264
A Vietnamese Genetic Variation Database Global Study-wide 212 G=0.802 A=0.198
The Danish reference pan genome Danish Study-wide 40 G=0.60 A=0.40
Siberian Global Study-wide 28 G=0.43 A=0.57
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 18 NC_000018.10:g.56039476G>A
GRCh37.p13 chr 18 NC_000018.9:g.53706707G>A
Gene: LOC642484, uncharacterized LOC642484 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
LINC03069 transcript NR_148972.1: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
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
GRCh38.p14 chr 18 NC_000018.10:g.56039476= NC_000018.10:g.56039476G>A
GRCh37.p13 chr 18 NC_000018.9:g.53706707= NC_000018.9:g.53706707G>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#.

65 SubSNP, 21 Frequency submissions
No Submitter Submission ID Date (Build)
1 CSHL-HAPMAP ss19376512 Feb 28, 2004 (120)
2 SSAHASNP ss21451605 Apr 05, 2004 (121)
3 ABI ss44075304 Mar 14, 2006 (126)
4 AFFY ss76540289 Dec 08, 2007 (129)
5 BCMHGSC_JDW ss90804366 Mar 24, 2008 (129)
6 HUMANGENOME_JCVI ss96343653 Feb 06, 2009 (130)
7 KRIBB_YJKIM ss105056480 Feb 06, 2009 (130)
8 ENSEMBL ss136398851 Dec 01, 2009 (131)
9 ENSEMBL ss137400354 Dec 01, 2009 (131)
10 COMPLETE_GENOMICS ss168293277 Jul 04, 2010 (132)
11 1000GENOMES ss211895232 Jul 14, 2010 (132)
12 1000GENOMES ss227890873 Jul 14, 2010 (132)
13 1000GENOMES ss237489683 Jul 15, 2010 (132)
14 1000GENOMES ss243733992 Jul 15, 2010 (132)
15 GMI ss283011897 May 04, 2012 (137)
16 PJP ss292079695 May 09, 2011 (134)
17 TISHKOFF ss565676850 Apr 25, 2013 (138)
18 SSMP ss661512511 Apr 25, 2013 (138)
19 EVA-GONL ss993789532 Aug 21, 2014 (142)
20 JMKIDD_LAB ss1081545333 Aug 21, 2014 (142)
21 1000GENOMES ss1361263976 Aug 21, 2014 (142)
22 DDI ss1428236444 Apr 01, 2015 (144)
23 EVA_GENOME_DK ss1578429318 Apr 01, 2015 (144)
24 EVA_UK10K_ALSPAC ss1637005571 Apr 01, 2015 (144)
25 EVA_UK10K_TWINSUK ss1679999604 Apr 01, 2015 (144)
26 EVA_DECODE ss1697851712 Apr 01, 2015 (144)
27 EVA_SVP ss1713630503 Apr 01, 2015 (144)
28 WEILL_CORNELL_DGM ss1937257136 Feb 12, 2016 (147)
29 GENOMED ss1968537884 Jul 19, 2016 (147)
30 JJLAB ss2029398624 Sep 14, 2016 (149)
31 USC_VALOUEV ss2157905995 Dec 20, 2016 (150)
32 HUMAN_LONGEVITY ss2222072009 Dec 20, 2016 (150)
33 ILLUMINA ss2633480031 Nov 08, 2017 (151)
34 GRF ss2702496460 Nov 08, 2017 (151)
35 GNOMAD ss2957362635 Nov 08, 2017 (151)
36 SWEGEN ss3016622994 Nov 08, 2017 (151)
37 BIOINF_KMB_FNS_UNIBA ss3028528944 Nov 08, 2017 (151)
38 CSHL ss3352050437 Nov 08, 2017 (151)
39 URBANLAB ss3650802607 Oct 12, 2018 (152)
40 EGCUT_WGS ss3683468911 Jul 13, 2019 (153)
41 EVA_DECODE ss3701776941 Jul 13, 2019 (153)
42 ACPOP ss3742594939 Jul 13, 2019 (153)
43 EVA ss3755465067 Jul 13, 2019 (153)
44 PACBIO ss3788387497 Jul 13, 2019 (153)
45 PACBIO ss3793316514 Jul 13, 2019 (153)
46 PACBIO ss3798202953 Jul 13, 2019 (153)
47 KHV_HUMAN_GENOMES ss3820720971 Jul 13, 2019 (153)
48 EVA ss3835199326 Apr 27, 2020 (154)
49 SGDP_PRJ ss3887140876 Apr 27, 2020 (154)
50 KRGDB ss3937027807 Apr 27, 2020 (154)
51 KOGIC ss3980261605 Apr 27, 2020 (154)
52 TOPMED ss5058832384 Apr 26, 2021 (155)
53 TOMMO_GENOMICS ss5225439625 Apr 26, 2021 (155)
54 1000G_HIGH_COVERAGE ss5305499162 Oct 16, 2022 (156)
55 EVA ss5431804167 Oct 16, 2022 (156)
56 HUGCELL_USP ss5498246269 Oct 16, 2022 (156)
57 EVA ss5511961830 Oct 16, 2022 (156)
58 1000G_HIGH_COVERAGE ss5610451011 Oct 16, 2022 (156)
59 SANFORD_IMAGENETICS ss5661412118 Oct 16, 2022 (156)
60 TOMMO_GENOMICS ss5783308306 Oct 16, 2022 (156)
61 YY_MCH ss5817150125 Oct 16, 2022 (156)
62 EVA ss5827626385 Oct 16, 2022 (156)
63 EVA ss5852078009 Oct 16, 2022 (156)
64 EVA ss5874324889 Oct 16, 2022 (156)
65 EVA ss5952834791 Oct 16, 2022 (156)
66 1000Genomes NC_000018.9 - 53706707 Oct 12, 2018 (152)
67 1000Genomes_30x NC_000018.10 - 56039476 Oct 16, 2022 (156)
68 The Avon Longitudinal Study of Parents and Children NC_000018.9 - 53706707 Oct 12, 2018 (152)
69 Chileans NC_000018.9 - 53706707 Apr 27, 2020 (154)
70 Genetic variation in the Estonian population NC_000018.9 - 53706707 Oct 12, 2018 (152)
71 The Danish reference pan genome NC_000018.9 - 53706707 Apr 27, 2020 (154)
72 gnomAD - Genomes NC_000018.10 - 56039476 Apr 26, 2021 (155)
73 Genome of the Netherlands Release 5 NC_000018.9 - 53706707 Apr 27, 2020 (154)
74 HapMap NC_000018.10 - 56039476 Apr 27, 2020 (154)
75 KOREAN population from KRGDB NC_000018.9 - 53706707 Apr 27, 2020 (154)
76 Korean Genome Project NC_000018.10 - 56039476 Apr 27, 2020 (154)
77 Northern Sweden NC_000018.9 - 53706707 Jul 13, 2019 (153)
78 Qatari NC_000018.9 - 53706707 Apr 27, 2020 (154)
79 SGDP_PRJ NC_000018.9 - 53706707 Apr 27, 2020 (154)
80 Siberian NC_000018.9 - 53706707 Apr 27, 2020 (154)
81 8.3KJPN NC_000018.9 - 53706707 Apr 26, 2021 (155)
82 14KJPN NC_000018.10 - 56039476 Oct 16, 2022 (156)
83 TopMed NC_000018.10 - 56039476 Apr 26, 2021 (155)
84 UK 10K study - Twins NC_000018.9 - 53706707 Oct 12, 2018 (152)
85 A Vietnamese Genetic Variation Database NC_000018.9 - 53706707 Jul 13, 2019 (153)
86 ALFA NC_000018.10 - 56039476 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
ss90804366, ss168293277, ss211895232, ss283011897, ss292079695, ss1697851712, ss1713630503 NC_000018.8:51857704:G:A NC_000018.10:56039475:G:A (self)
74601273, 41341493, 196502, 29207159, 4620283, 18415995, 44205201, 15879804, 19299058, 39157856, 10422349, 83408932, 41341493, 9134071, ss227890873, ss237489683, ss243733992, ss565676850, ss661512511, ss993789532, ss1081545333, ss1361263976, ss1428236444, ss1578429318, ss1637005571, ss1679999604, ss1937257136, ss1968537884, ss2029398624, ss2157905995, ss2633480031, ss2702496460, ss2957362635, ss3016622994, ss3352050437, ss3683468911, ss3742594939, ss3755465067, ss3788387497, ss3793316514, ss3798202953, ss3835199326, ss3887140876, ss3937027807, ss5225439625, ss5431804167, ss5511961830, ss5661412118, ss5827626385, ss5952834791 NC_000018.9:53706706:G:A NC_000018.10:56039475:G:A (self)
97976946, 526274552, 1613976, 36639606, 117145410, 274378047, 13284825283, ss2222072009, ss3028528944, ss3650802607, ss3701776941, ss3820720971, ss3980261605, ss5058832384, ss5305499162, ss5498246269, ss5610451011, ss5783308306, ss5817150125, ss5852078009, ss5874324889 NC_000018.10:56039475:G:A NC_000018.10:56039475:G:A (self)
ss19376512, ss21451605 NT_025028.13:1497570:G:A NC_000018.10:56039475:G:A (self)
ss44075304, ss76540289, ss96343653, ss105056480, ss136398851, ss137400354 NT_025028.14:1497570:G:A NC_000018.10:56039475:G:A (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 rs12454530

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