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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.


Current Build 155

Released April 9, 2021

Homo sapiens
chr1:55049283 (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.

G>A / G>C
Variation Type
SNV Single Nucleotide Variation
A=0.056508 (14957/264690, TOPMED)
A=0.053717 (7534/140254, GnomAD)
A=0.00006 (1/16760, 8.3KJPN) (+ 9 more)
A=0.00887 (121/13638, ALFA)
A=0.0545 (273/5008, 1000G)
A=0.0003 (1/3854, ALSPAC)
A=0.0003 (1/3708, TWINSUK)
A=0.001 (1/998, GoNL)
A=0.002 (1/600, NorthernSweden)
A=0.047 (15/318, HapMap)
A=0.014 (3/216, Qatari)
G=0.37 (11/30, SGDP_PRJ)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
PCSK9 : Intron Variant
2 citations
Genomic View
See rs on genome

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.55049283G>A
GRCh38.p13 chr 1 NC_000001.11:g.55049283G>C
GRCh37.p13 chr 1 NC_000001.10:g.55514956G>A
GRCh37.p13 chr 1 NC_000001.10:g.55514956G>C
PCSK9 RefSeqGene (LRG_275) NG_009061.1:g.14737G>A
PCSK9 RefSeqGene (LRG_275) NG_009061.1:g.14737G>C
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.523+2637G>A N/A Intron Variant
PCSK9 transcript variant 2 NR_110451.2:n. N/A Intron Variant

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 13638 G=0.99113 A=0.00887, C=0.00000
European Sub 9802 G=0.9997 A=0.0003, C=0.0000
African Sub 2238 G=0.9495 A=0.0505, C=0.0000
African Others Sub 86 G=0.93 A=0.07, C=0.00
African American Sub 2152 G=0.9503 A=0.0497, C=0.0000
Asian Sub 112 G=1.000 A=0.000, C=0.000
East Asian Sub 86 G=1.00 A=0.00, C=0.00
Other Asian Sub 26 G=1.00 A=0.00, C=0.00
Latin American 1 Sub 142 G=1.000 A=0.000, C=0.000
Latin American 2 Sub 596 G=1.000 A=0.000, C=0.000
South Asian Sub 98 G=1.00 A=0.00, C=0.00
Other Sub 650 G=0.992 A=0.008, C=0.000


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").

Study Population Group Sample Size Ref Allele Alt Allele
TopMed Global Study-wide 264690 G=0.943492 A=0.056508
gnomAD - Genomes Global Study-wide 140254 G=0.946283 A=0.053717
gnomAD - Genomes European Sub 75960 G=0.99947 A=0.00053
gnomAD - Genomes African Sub 42018 G=0.82907 A=0.17093
gnomAD - Genomes American Sub 13664 G=0.98434 A=0.01566
gnomAD - Genomes Ashkenazi Jewish Sub 3324 G=0.9976 A=0.0024
gnomAD - Genomes East Asian Sub 3134 G=0.9997 A=0.0003
gnomAD - Genomes Other Sub 2154 G=0.9587 A=0.0413
8.3KJPN JAPANESE Study-wide 16760 G=0.99994 A=0.00006
1000Genomes Global Study-wide 5008 G=0.9455 A=0.0545
1000Genomes African Sub 1322 G=0.8033 A=0.1967
1000Genomes East Asian Sub 1008 G=1.0000 A=0.0000
1000Genomes Europe Sub 1006 G=0.9980 A=0.0020
1000Genomes South Asian Sub 978 G=1.000 A=0.000
1000Genomes American Sub 694 G=0.984 A=0.016
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.9997 A=0.0003
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.9997 A=0.0003
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.999 A=0.001
Northern Sweden ACPOP Study-wide 600 G=0.998 A=0.002
HapMap Global Study-wide 318 G=0.953 A=0.047
HapMap American Sub 120 G=1.000 A=0.000
HapMap African Sub 108 G=0.861 A=0.139
HapMap Asian Sub 90 G=1.00 A=0.00
Qatari Global Study-wide 216 G=0.986 A=0.014
SGDP_PRJ Global Study-wide 30 G=0.37 A=0.63

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.55049283= NC_000001.11:g.55049283G>A NC_000001.11:g.55049283G>C
GRCh37.p13 chr 1 NC_000001.10:g.55514956= NC_000001.10:g.55514956G>A NC_000001.10:g.55514956G>C
PCSK9 RefSeqGene (LRG_275) NG_009061.1:g.14737= NG_009061.1:g.14737G>A NG_009061.1:g.14737G>C
PCSK9 transcript variant 1 NM_174936.3:c.523+2637= NM_174936.3:c.523+2637G>A NM_174936.3:c.523+2637G>C
PCSK9 transcript variant 1 NM_174936.4:c.523+2637= NM_174936.4:c.523+2637G>A NM_174936.4:c.523+2637G>C

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#.

27 SubSNP, 12 Frequency submissions
No Submitter Submission ID Date (Build)
1 WI_SSAHASNP ss11351688 Jul 11, 2003 (116)
2 PGA-UW-FHCRC ss35032266 May 24, 2005 (125)
3 PGA-UW-FHCRC ss52088204 Oct 13, 2006 (127)
4 1000GENOMES ss110458260 Jan 24, 2009 (130)
5 ILLUMINA-UK ss118698276 Feb 14, 2009 (130)
6 COMPLETE_GENOMICS ss163394700 Jul 04, 2010 (132)
7 BUSHMAN ss198458339 Jul 04, 2010 (132)
8 1000GENOMES ss218385313 Jul 14, 2010 (132)
9 TISHKOFF ss554113652 Apr 25, 2013 (138)
10 EVA-GONL ss975160970 Aug 21, 2014 (142)
11 JMKIDD_LAB ss1067886650 Aug 21, 2014 (142)
12 1000GENOMES ss1290895560 Aug 21, 2014 (142)
13 EVA_UK10K_ALSPAC ss1600174778 Apr 01, 2015 (144)
14 EVA_UK10K_TWINSUK ss1643168811 Apr 01, 2015 (144)
15 WEILL_CORNELL_DGM ss1918369783 Feb 12, 2016 (147)
16 HUMAN_LONGEVITY ss2162510879 Dec 20, 2016 (150)
17 TOPMED ss2324751205 Dec 20, 2016 (150)
18 GNOMAD ss2755161155 Nov 08, 2017 (151)
19 SWEGEN ss2986818973 Nov 08, 2017 (151)
20 TOPMED ss3076674343 Nov 08, 2017 (151)
21 EVA_DECODE ss3686773604 Jul 12, 2019 (153)
22 ACPOP ss3727047675 Jul 12, 2019 (153)
23 KHV_HUMAN_GENOMES ss3799213970 Jul 12, 2019 (153)
24 EVA ss3826172000 Apr 25, 2020 (154)
25 SGDP_PRJ ss3848848200 Apr 25, 2020 (154)
26 TOPMED ss4449767236 Apr 25, 2021 (155)
27 TOMMO_GENOMICS ss5143955354 Apr 25, 2021 (155)
28 1000Genomes NC_000001.10 - 55514956 Oct 11, 2018 (152)
29 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 55514956 Oct 11, 2018 (152)
30 gnomAD - Genomes NC_000001.11 - 55049283 Apr 25, 2021 (155)
31 Genome of the Netherlands Release 5 NC_000001.10 - 55514956 Apr 25, 2020 (154)
32 HapMap NC_000001.11 - 55049283 Apr 25, 2020 (154)
33 Northern Sweden NC_000001.10 - 55514956 Jul 12, 2019 (153)
34 Qatari NC_000001.10 - 55514956 Apr 25, 2020 (154)
35 SGDP_PRJ NC_000001.10 - 55514956 Apr 25, 2020 (154)
36 8.3KJPN NC_000001.10 - 55514956 Apr 25, 2021 (155)
37 TopMed NC_000001.11 - 55049283 Apr 25, 2021 (155)
38 UK 10K study - Twins NC_000001.10 - 55514956 Oct 11, 2018 (152)
39 ALFA NC_000001.11 - 55049283 Apr 25, 2021 (155)

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
ss110458260, ss118698276, ss163394700, ss198458339 NC_000001.9:55287543:G:A NC_000001.11:55049282:G:A (self)
1614089, 877967, 372352, 332540, 411713, 865180, 1924661, 877967, ss218385313, ss554113652, ss975160970, ss1067886650, ss1290895560, ss1600174778, ss1643168811, ss1918369783, ss2324751205, ss2755161155, ss2986818973, ss3727047675, ss3826172000, ss3848848200, ss5143955354 NC_000001.10:55514955:G:A NC_000001.11:55049282:G:A (self)
11422168, 68170, 8416968, 13373571, 12273147288, ss2162510879, ss3076674343, ss3686773604, ss3799213970, ss4449767236 NC_000001.11:55049282:G:A NC_000001.11:55049282:G:A (self)
ss11351688 NT_032977.5:7963867:G:A NC_000001.11:55049282:G:A (self)
ss35032266, ss52088204 NT_032977.9:25486873:G:A NC_000001.11:55049282:G:A (self)
12273147288 NC_000001.11:55049282:G:C NC_000001.11:55049282:G:C

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

2 citations for rs7517090
PMID Title Author Year Journal
20308432 Association analysis of 33 lipoprotein candidate genes in multi-generational families of African ancestry. Miljkovic I et al. 2010 Journal of lipid research
21862702 Mechanisms and genetic determinants regulating sterol absorption, circulating LDL levels, and sterol elimination: implications for classification and disease risk. Calandra S et al. 2011 Journal of lipid research

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