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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.

rs11800231

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:55052267 (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>T
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.086222 (22822/264690, TOPMED)
A=0.052203 (13121/251344, GnomAD_exome)
A=0.081514 (11418/140074, GnomAD) (+ 19 more)
A=0.054904 (6661/121320, ExAC)
A=0.06552 (2836/43284, ALFA)
A=0.02226 (373/16760, 8.3KJPN)
A=0.08788 (1143/13006, GO-ESP)
A=0.0829 (415/5008, 1000G)
A=0.0324 (145/4480, Estonian)
A=0.0459 (177/3854, ALSPAC)
A=0.0494 (183/3708, TWINSUK)
A=0.0264 (77/2922, KOREAN)
A=0.0300 (55/1832, Korea1K)
A=0.039 (39/998, GoNL)
A=0.042 (26/616, Vietnamese)
A=0.053 (32/600, NorthernSweden)
A=0.047 (25/534, MGP)
A=0.023 (7/304, FINRISK)
A=0.167 (36/216, Qatari)
G=0.47 (42/90, SGDP_PRJ)
A=0.03 (1/40, GENOME_DK)
G=0.3 (2/6, Siberian)
Clinical Significance
Reported in ClinVar
Gene : Consequence
PCSK9 : Intron Variant
Publications
3 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.55052267G>A
GRCh38.p13 chr 1 NC_000001.11:g.55052267G>T
GRCh37.p13 chr 1 NC_000001.10:g.55517940G>A
GRCh37.p13 chr 1 NC_000001.10:g.55517940G>T
PCSK9 RefSeqGene (LRG_275) NG_009061.1:g.17721G>A
PCSK9 RefSeqGene (LRG_275) NG_009061.1:g.17721G>T
Gene: PCSK9, proprotein convertase subtilisin/kexin type 9 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
PCSK9 transcript variant 1 NM_174936.4:c.524-11G>A N/A Intron Variant
PCSK9 transcript variant 2 NR_110451.2: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.

Allele: A (allele ID: 45332 )
ClinVar Accession Disease Names Clinical Significance
RCV000030350.5 Familial hypercholesterolemia 1 Benign
RCV000253452.2 not specified Benign
RCV000289127.2 Hypobetalipoproteinemia Benign
RCV000609330.2 Familial hypercholesterolemia 3 Benign

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 43284 G=0.93448 A=0.06552
European Sub 33020 G=0.95039 A=0.04961
African Sub 4890 G=0.8333 A=0.1667
African Others Sub 162 G=0.821 A=0.179
African American Sub 4728 G=0.8338 A=0.1662
Asian Sub 184 G=0.962 A=0.038
East Asian Sub 126 G=0.968 A=0.032
Other Asian Sub 58 G=0.95 A=0.05
Latin American 1 Sub 168 G=0.929 A=0.071
Latin American 2 Sub 700 G=0.959 A=0.041
South Asian Sub 114 G=0.947 A=0.053
Other Sub 4208 G=0.9218 A=0.0782


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=0.913778 A=0.086222
gnomAD - Exomes Global Study-wide 251344 G=0.947797 A=0.052203
gnomAD - Exomes European Sub 135274 G=0.958152 A=0.041848
gnomAD - Exomes Asian Sub 49008 G=0.96117 A=0.03883
gnomAD - Exomes American Sub 34592 G=0.96580 A=0.03420
gnomAD - Exomes African Sub 16256 G=0.81736 A=0.18264
gnomAD - Exomes Ashkenazi Jewish Sub 10078 G=0.89423 A=0.10577
gnomAD - Exomes Other Sub 6136 G=0.9448 A=0.0552
gnomAD - Genomes Global Study-wide 140074 G=0.918486 A=0.081514
gnomAD - Genomes European Sub 75918 G=0.96076 A=0.03924
gnomAD - Genomes African Sub 41930 G=0.82726 A=0.17274
gnomAD - Genomes American Sub 13628 G=0.95487 A=0.04513
gnomAD - Genomes Ashkenazi Jewish Sub 3318 G=0.8987 A=0.1013
gnomAD - Genomes East Asian Sub 3128 G=0.9703 A=0.0297
gnomAD - Genomes Other Sub 2152 G=0.9294 A=0.0706
ExAC Global Study-wide 121320 G=0.945096 A=0.054904
ExAC Europe Sub 73278 G=0.95438 A=0.04562
ExAC Asian Sub 25160 G=0.96002 A=0.03998
ExAC American Sub 11574 G=0.96587 A=0.03413
ExAC African Sub 10402 G=0.82013 A=0.17987
ExAC Other Sub 906 G=0.949 A=0.051
8.3KJPN JAPANESE Study-wide 16760 G=0.97774 A=0.02226
GO Exome Sequencing Project Global Study-wide 13006 G=0.91212 A=0.08788
GO Exome Sequencing Project European American Sub 8600 G=0.9542 A=0.0458
GO Exome Sequencing Project African American Sub 4406 G=0.8300 A=0.1700
1000Genomes Global Study-wide 5008 G=0.9171 A=0.0829
1000Genomes African Sub 1322 G=0.8101 A=0.1899
1000Genomes East Asian Sub 1008 G=0.9732 A=0.0268
1000Genomes Europe Sub 1006 G=0.9473 A=0.0527
1000Genomes South Asian Sub 978 G=0.952 A=0.048
1000Genomes American Sub 694 G=0.947 A=0.053
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.9676 A=0.0324
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.9541 A=0.0459
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.9506 A=0.0494
KOREAN population from KRGDB KOREAN Study-wide 2922 G=0.9736 A=0.0264
Korean Genome Project KOREAN Study-wide 1832 G=0.9700 A=0.0300
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.961 A=0.039
A Vietnamese Genetic Variation Database Global Study-wide 616 G=0.958 A=0.042
Northern Sweden ACPOP Study-wide 600 G=0.947 A=0.053
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 G=0.953 A=0.047
FINRISK Finnish from FINRISK project Study-wide 304 G=0.977 A=0.023
Qatari Global Study-wide 216 G=0.833 A=0.167
SGDP_PRJ Global Study-wide 90 G=0.47 A=0.53
The Danish reference pan genome Danish Study-wide 40 G=0.97 A=0.03
Siberian Global Study-wide 6 G=0.3 A=0.7
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 T
GRCh38.p13 chr 1 NC_000001.11:g.55052267= NC_000001.11:g.55052267G>A NC_000001.11:g.55052267G>T
GRCh37.p13 chr 1 NC_000001.10:g.55517940= NC_000001.10:g.55517940G>A NC_000001.10:g.55517940G>T
PCSK9 RefSeqGene (LRG_275) NG_009061.1:g.17721= NG_009061.1:g.17721G>A NG_009061.1:g.17721G>T
PCSK9 transcript variant 1 NM_174936.3:c.524-11= NM_174936.3:c.524-11G>A NM_174936.3:c.524-11G>T
PCSK9 transcript variant 1 NM_174936.4:c.524-11= NM_174936.4:c.524-11G>A NM_174936.4:c.524-11G>T
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#.

76 SubSNP, 22 Frequency, 4 ClinVar submissions
No Submitter Submission ID Date (Build)
1 CSHL-HAPMAP ss17328219 Feb 28, 2004 (120)
2 ABI ss44121425 Mar 13, 2006 (126)
3 PGA-UW-FHCRC ss69358636 May 17, 2007 (127)
4 HGSV ss85379099 Dec 14, 2007 (130)
5 BCMHGSC_JDW ss87438158 Mar 23, 2008 (129)
6 RSG_UW ss107937140 Feb 04, 2009 (130)
7 ILLUMINA-UK ss118698310 Feb 14, 2009 (130)
8 ENSEMBL ss137940382 Dec 01, 2009 (131)
9 ILLUMINA ss171590557 Jul 04, 2010 (132)
10 BUSHMAN ss198458367 Jul 04, 2010 (132)
11 1000GENOMES ss210526295 Jul 14, 2010 (132)
12 1000GENOMES ss218385335 Jul 14, 2010 (132)
13 1000GENOMES ss230534732 Jul 14, 2010 (132)
14 1000GENOMES ss238229163 Jul 15, 2010 (132)
15 ILLUMINA ss244274101 Jul 04, 2010 (132)
16 GMI ss275826971 May 04, 2012 (137)
17 CORRELAGEN ss475577420 Nov 18, 2011 (136)
18 ILLUMINA ss482361086 May 04, 2012 (137)
19 ILLUMINA ss483762870 May 04, 2012 (137)
20 1000GENOMES ss489745018 May 04, 2012 (137)
21 CLINSEQ_SNP ss491595468 May 04, 2012 (137)
22 ILLUMINA ss535962142 Sep 08, 2015 (146)
23 TISHKOFF ss554113682 Apr 25, 2013 (138)
24 SSMP ss647944639 Apr 25, 2013 (138)
25 NHLBI-ESP ss712314315 Apr 25, 2013 (138)
26 ILLUMINA ss780399253 Sep 08, 2015 (146)
27 ILLUMINA ss782325023 Sep 08, 2015 (146)
28 ILLUMINA ss835888031 Sep 08, 2015 (146)
29 EVA-GONL ss975160993 Aug 21, 2014 (142)
30 JMKIDD_LAB ss1067421702 Aug 21, 2014 (142)
31 JMKIDD_LAB ss1067886678 Aug 21, 2014 (142)
32 1000GENOMES ss1290895664 Aug 21, 2014 (142)
33 DDI ss1425808431 Apr 01, 2015 (144)
34 EVA_GENOME_DK ss1574059297 Apr 01, 2015 (144)
35 EVA_FINRISK ss1584008251 Apr 01, 2015 (144)
36 EVA_DECODE ss1584527322 Apr 01, 2015 (144)
37 EVA_UK10K_ALSPAC ss1600174839 Apr 01, 2015 (144)
38 EVA_UK10K_TWINSUK ss1643168872 Apr 01, 2015 (144)
39 EVA_MGP ss1710906309 Apr 01, 2015 (144)
40 HAMMER_LAB ss1794365776 Sep 08, 2015 (146)
41 WEILL_CORNELL_DGM ss1918369816 Feb 12, 2016 (147)
42 JJLAB ss2019700503 Sep 14, 2016 (149)
43 ILLUMINA ss2094783090 Dec 20, 2016 (150)
44 USC_VALOUEV ss2147714840 Dec 20, 2016 (150)
45 HUMAN_LONGEVITY ss2162511093 Dec 20, 2016 (150)
46 TOPMED ss2324751401 Dec 20, 2016 (150)
47 ILLUMINA ss2632515474 Nov 08, 2017 (151)
48 GRF ss2697627251 Nov 08, 2017 (151)
49 SWEGEN ss2986819010 Nov 08, 2017 (151)
50 TOPMED ss3076674897 Nov 08, 2017 (151)
51 CSHL ss3343453943 Nov 08, 2017 (151)
52 ILLUMINA ss3626098033 Oct 11, 2018 (152)
53 ILLUMINA ss3630551665 Oct 11, 2018 (152)
54 ILLUMINA ss3637756845 Oct 11, 2018 (152)
55 ILLUMINA ss3641589276 Oct 11, 2018 (152)
56 OMUKHERJEE_ADBS ss3646231059 Oct 11, 2018 (152)
57 EGCUT_WGS ss3654882610 Jul 12, 2019 (153)
58 EVA_DECODE ss3686773648 Jul 12, 2019 (153)
59 ACPOP ss3727047699 Jul 12, 2019 (153)
60 EVA ss3746204741 Jul 12, 2019 (153)
61 PACBIO ss3783409023 Jul 12, 2019 (153)
62 PACBIO ss3789066998 Jul 12, 2019 (153)
63 PACBIO ss3793939695 Jul 12, 2019 (153)
64 KHV_HUMAN_GENOMES ss3799214014 Jul 12, 2019 (153)
65 EVA ss3823615303 Apr 25, 2020 (154)
66 EVA ss3825565661 Apr 25, 2020 (154)
67 EVA ss3826172017 Apr 25, 2020 (154)
68 SGDP_PRJ ss3848848269 Apr 25, 2020 (154)
69 KRGDB ss3893859025 Apr 25, 2020 (154)
70 KOGIC ss3944514734 Apr 25, 2020 (154)
71 FSA-LAB ss3983932412 Apr 25, 2021 (155)
72 FSA-LAB ss3983932413 Apr 25, 2021 (155)
73 EVA ss3986121380 Apr 25, 2021 (155)
74 GNOMAD ss3993677593 Apr 25, 2021 (155)
75 TOPMED ss4449768008 Apr 25, 2021 (155)
76 TOMMO_GENOMICS ss5143955445 Apr 25, 2021 (155)
77 1000Genomes NC_000001.10 - 55517940 Oct 11, 2018 (152)
78 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 55517940 Oct 11, 2018 (152)
79 Genetic variation in the Estonian population NC_000001.10 - 55517940 Oct 11, 2018 (152)
80 ExAC NC_000001.10 - 55517940 Oct 11, 2018 (152)
81 FINRISK NC_000001.10 - 55517940 Apr 25, 2020 (154)
82 The Danish reference pan genome NC_000001.10 - 55517940 Apr 25, 2020 (154)
83 gnomAD - Genomes NC_000001.11 - 55052267 Apr 25, 2021 (155)
84 gnomAD - Exomes NC_000001.10 - 55517940 Jul 12, 2019 (153)
85 GO Exome Sequencing Project NC_000001.10 - 55517940 Oct 11, 2018 (152)
86 Genome of the Netherlands Release 5 NC_000001.10 - 55517940 Apr 25, 2020 (154)
87 KOREAN population from KRGDB NC_000001.10 - 55517940 Apr 25, 2020 (154)
88 Korean Genome Project NC_000001.11 - 55052267 Apr 25, 2020 (154)
89 Medical Genome Project healthy controls from Spanish population NC_000001.10 - 55517940 Apr 25, 2020 (154)
90 Northern Sweden NC_000001.10 - 55517940 Jul 12, 2019 (153)
91 Qatari NC_000001.10 - 55517940 Apr 25, 2020 (154)
92 SGDP_PRJ NC_000001.10 - 55517940 Apr 25, 2020 (154)
93 Siberian NC_000001.10 - 55517940 Apr 25, 2020 (154)
94 8.3KJPN NC_000001.10 - 55517940 Apr 25, 2021 (155)
95 TopMed NC_000001.11 - 55052267 Apr 25, 2021 (155)
96 UK 10K study - Twins NC_000001.10 - 55517940 Oct 11, 2018 (152)
97 A Vietnamese Genetic Variation Database NC_000001.10 - 55517940 Jul 12, 2019 (153)
98 ALFA NC_000001.11 - 55052267 Apr 25, 2021 (155)
99 ClinVar RCV000030350.5 Apr 25, 2021 (155)
100 ClinVar RCV000253452.2 Oct 11, 2018 (152)
101 ClinVar RCV000289127.2 Apr 25, 2021 (155)
102 ClinVar RCV000609330.2 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).

Associated ID History Updated (Build)
rs58022626 May 24, 2008 (130)
rs116999275 Aug 16, 2010 (132)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss85379099 NC_000001.8:55229960:G:A NC_000001.11:55052266:G:A (self)
ss87438158, ss118698310, ss198458367, ss210526295, ss275826971, ss482361086, ss491595468, ss1584527322 NC_000001.9:55290527:G:A NC_000001.11:55052266:G:A (self)
1614199, 878031, 620858, 4763154, 4712, 1501777, 543603, 73970, 372375, 1036419, 23061, 332564, 411746, 865249, 231194, 1924752, 878031, 180150, ss218385335, ss230534732, ss238229163, ss483762870, ss489745018, ss535962142, ss554113682, ss647944639, ss712314315, ss780399253, ss782325023, ss835888031, ss975160993, ss1067421702, ss1067886678, ss1290895664, ss1425808431, ss1574059297, ss1584008251, ss1600174839, ss1643168872, ss1710906309, ss1794365776, ss1918369816, ss2019700503, ss2094783090, ss2147714840, ss2324751401, ss2632515474, ss2697627251, ss2986819010, ss3343453943, ss3626098033, ss3630551665, ss3637756845, ss3641589276, ss3646231059, ss3654882610, ss3727047699, ss3746204741, ss3783409023, ss3789066998, ss3793939695, ss3823615303, ss3825565661, ss3826172017, ss3848848269, ss3893859025, ss3983932412, ss3983932413, ss3986121380, ss5143955445 NC_000001.10:55517939:G:A NC_000001.11:55052266:G:A (self)
RCV000030350.5, RCV000253452.2, RCV000289127.2, RCV000609330.2, 11422777, 892735, 8417482, 13374343, 4195513326, ss475577420, ss2162511093, ss3076674897, ss3686773648, ss3799214014, ss3944514734, ss3993677593, ss4449768008 NC_000001.11:55052266:G:A NC_000001.11:55052266:G:A (self)
ss17328219 NT_032977.6:17081010:G:A NC_000001.11:55052266:G:A (self)
ss44121425, ss69358636, ss107937140, ss137940382, ss171590557, ss244274101 NT_032977.9:25489857:G:A NC_000001.11:55052266:G:A (self)
ss107937140 NT_032977.9:25489857:G:T NC_000001.11:55052266:G:T (self)
Help

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

3 citations for rs11800231
PMID Title Author Year Journal
12730697 Mutations in PCSK9 cause autosomal dominant hypercholesterolemia. Abifadel M et al. 2003 Nature genetics
23236364 Gene-centric meta-analysis of lipid traits in African, East Asian and Hispanic populations. Elbers CC et al. 2012 PloS one
25741868 Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Richards S et al. 2015 Genetics in medicine
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