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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.

rs147182054

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:55063480 (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
C>G / C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.000038 (10/264690, TOPMED)
T=0.000043 (6/140268, GnomAD)
T=0.00006 (5/78692, PAGE_STUDY) (+ 6 more)
G=0.00012 (2/16760, 8.3KJPN)
T=0.00008 (1/13006, GO-ESP)
T=0.00008 (1/12522, ALFA)
T=0.0002 (1/5008, 1000G)
G=0.0007 (2/2920, KOREAN)
G=0.0005 (1/1832, Korea1K)
Clinical Significance
Reported in ClinVar
Gene : Consequence
PCSK9 : Missense 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.55063480C>G
GRCh38.p13 chr 1 NC_000001.11:g.55063480C>T
GRCh37.p13 chr 1 NC_000001.10:g.55529153C>G
GRCh37.p13 chr 1 NC_000001.10:g.55529153C>T
PCSK9 RefSeqGene (LRG_275) NG_009061.1:g.28934C>G
PCSK9 RefSeqGene (LRG_275) NG_009061.1:g.28934C>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.1975C>G R [CGG] > G [GGG] Coding Sequence Variant
proprotein convertase subtilisin/kexin type 9 preproprotein NP_777596.2:p.Arg659Gly R (Arg) > G (Gly) Missense Variant
PCSK9 transcript variant 1 NM_174936.4:c.1975C>T R [CGG] > W [TGG] Coding Sequence Variant
proprotein convertase subtilisin/kexin type 9 preproprotein NP_777596.2:p.Arg659Trp R (Arg) > W (Trp) Missense Variant
PCSK9 transcript variant 2 NR_110451.2:n.1582C>G N/A Non Coding Transcript Variant
PCSK9 transcript variant 2 NR_110451.2:n.1582C>T N/A Non Coding 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.

Allele: T (allele ID: 907505 )
ClinVar Accession Disease Names Clinical Significance
RCV001186682.1 Familial hypercholesterolemia Uncertain-Significance

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 12522 C=0.99992 T=0.00008
European Sub 7696 C=1.0000 T=0.0000
African Sub 3250 C=0.9997 T=0.0003
African Others Sub 108 C=1.000 T=0.000
African American Sub 3142 C=0.9997 T=0.0003
Asian Sub 142 C=1.000 T=0.000
East Asian Sub 118 C=1.000 T=0.000
Other Asian Sub 24 C=1.00 T=0.00
Latin American 1 Sub 146 C=1.000 T=0.000
Latin American 2 Sub 610 C=1.000 T=0.000
South Asian Sub 100 C=1.00 T=0.00
Other Sub 578 C=1.000 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=0.999962 T=0.000038
gnomAD - Genomes Global Study-wide 140268 C=0.999957 T=0.000043
gnomAD - Genomes European Sub 75948 C=0.99999 T=0.00001
gnomAD - Genomes African Sub 42048 C=0.99988 T=0.00012
gnomAD - Genomes American Sub 13666 C=1.00000 T=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3322 C=1.0000 T=0.0000
gnomAD - Genomes East Asian Sub 3134 C=1.0000 T=0.0000
gnomAD - Genomes Other Sub 2150 C=1.0000 T=0.0000
The PAGE Study Global Study-wide 78692 C=0.99994 T=0.00006
The PAGE Study AfricanAmerican Sub 32514 C=0.99985 T=0.00015
The PAGE Study Mexican Sub 10810 C=1.00000 T=0.00000
The PAGE Study Asian Sub 8314 C=1.0000 T=0.0000
The PAGE Study PuertoRican Sub 7918 C=1.0000 T=0.0000
The PAGE Study NativeHawaiian Sub 4530 C=1.0000 T=0.0000
The PAGE Study Cuban Sub 4230 C=1.0000 T=0.0000
The PAGE Study Dominican Sub 3828 C=1.0000 T=0.0000
The PAGE Study CentralAmerican Sub 2450 C=1.0000 T=0.0000
The PAGE Study SouthAmerican Sub 1982 C=1.0000 T=0.0000
The PAGE Study NativeAmerican Sub 1260 C=1.0000 T=0.0000
The PAGE Study SouthAsian Sub 856 C=1.000 T=0.000
8.3KJPN JAPANESE Study-wide 16760 C=0.99988 G=0.00012
GO Exome Sequencing Project Global Study-wide 13006 C=0.99992 T=0.00008
GO Exome Sequencing Project European American Sub 8600 C=1.0000 T=0.0000
GO Exome Sequencing Project African American Sub 4406 C=0.9998 T=0.0002
Allele Frequency Aggregator Total Global 12522 C=0.99992 T=0.00008
Allele Frequency Aggregator European Sub 7696 C=1.0000 T=0.0000
Allele Frequency Aggregator African Sub 3250 C=0.9997 T=0.0003
Allele Frequency Aggregator Latin American 2 Sub 610 C=1.000 T=0.000
Allele Frequency Aggregator Other Sub 578 C=1.000 T=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 C=1.000 T=0.000
Allele Frequency Aggregator Asian Sub 142 C=1.000 T=0.000
Allele Frequency Aggregator South Asian Sub 100 C=1.00 T=0.00
1000Genomes Global Study-wide 5008 C=0.9998 T=0.0002
1000Genomes African Sub 1322 C=0.9992 T=0.0008
1000Genomes East Asian Sub 1008 C=1.0000 T=0.0000
1000Genomes Europe Sub 1006 C=1.0000 T=0.0000
1000Genomes South Asian Sub 978 C=1.000 T=0.000
1000Genomes American Sub 694 C=1.000 T=0.000
KOREAN population from KRGDB KOREAN Study-wide 2920 C=0.9993 G=0.0007
Korean Genome Project KOREAN Study-wide 1832 C=0.9995 G=0.0005
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.p13 chr 1 NC_000001.11:g.55063480= NC_000001.11:g.55063480C>G NC_000001.11:g.55063480C>T
GRCh37.p13 chr 1 NC_000001.10:g.55529153= NC_000001.10:g.55529153C>G NC_000001.10:g.55529153C>T
PCSK9 RefSeqGene (LRG_275) NG_009061.1:g.28934= NG_009061.1:g.28934C>G NG_009061.1:g.28934C>T
PCSK9 transcript variant 1 NM_174936.4:c.1975= NM_174936.4:c.1975C>G NM_174936.4:c.1975C>T
PCSK9 transcript variant 1 NM_174936.3:c.1975= NM_174936.3:c.1975C>G NM_174936.3:c.1975C>T
PCSK9 transcript variant 2 NR_110451.2:n.1582= NR_110451.2:n.1582C>G NR_110451.2:n.1582C>T
PCSK9 transcript variant 2 NR_110451.1:n.1582= NR_110451.1:n.1582C>G NR_110451.1:n.1582C>T
proprotein convertase subtilisin/kexin type 9 preproprotein NP_777596.2:p.Arg659= NP_777596.2:p.Arg659Gly NP_777596.2:p.Arg659Trp
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#.

20 SubSNP, 13 Frequency, 1 ClinVar submissions
No Submitter Submission ID Date (Build)
1 NHLBI-ESP ss341966602 May 09, 2011 (134)
2 1000GENOMES ss488669567 May 04, 2012 (137)
3 1000GENOMES ss1290896042 Aug 21, 2014 (142)
4 EVA_EXAC ss1685565555 Apr 01, 2015 (144)
5 EVA_EXAC ss1685565556 Apr 01, 2015 (144)
6 ILLUMINA ss1958273616 Feb 12, 2016 (147)
7 TOPMED ss2324752166 Dec 20, 2016 (150)
8 GNOMAD ss2731525782 Nov 08, 2017 (151)
9 GNOMAD ss2746340040 Nov 08, 2017 (151)
10 GNOMAD ss2755162395 Nov 08, 2017 (151)
11 ILLUMINA ss3021088399 Nov 08, 2017 (151)
12 TOPMED ss3076677158 Nov 08, 2017 (151)
13 ILLUMINA ss3651414867 Oct 11, 2018 (152)
14 ILLUMINA ss3725025168 Jul 12, 2019 (153)
15 PAGE_CC ss3770809331 Jul 12, 2019 (153)
16 EVA ss3823615423 Apr 25, 2020 (154)
17 KRGDB ss3893859237 Apr 25, 2020 (154)
18 KOGIC ss3944514967 Apr 25, 2020 (154)
19 TOPMED ss4449770987 Apr 25, 2021 (155)
20 TOMMO_GENOMICS ss5143955840 Apr 25, 2021 (155)
21 1000Genomes NC_000001.10 - 55529153 Oct 11, 2018 (152)
22 ExAC

Submission ignored due to conflicting rows:
Row 4763653 (NC_000001.10:55529152:C:C 120505/120508, NC_000001.10:55529152:C:T 3/120508)
Row 4763654 (NC_000001.10:55529152:C:C 120504/120508, NC_000001.10:55529152:C:G 4/120508)

- Oct 11, 2018 (152)
23 ExAC

Submission ignored due to conflicting rows:
Row 4763653 (NC_000001.10:55529152:C:C 120505/120508, NC_000001.10:55529152:C:T 3/120508)
Row 4763654 (NC_000001.10:55529152:C:C 120504/120508, NC_000001.10:55529152:C:G 4/120508)

- Oct 11, 2018 (152)
24 gnomAD - Genomes NC_000001.11 - 55063480 Apr 25, 2021 (155)
25 gnomAD - Exomes

Submission ignored due to conflicting rows:
Row 544313 (NC_000001.10:55529152:C:C 250944/250948, NC_000001.10:55529152:C:G 4/250948)
Row 544314 (NC_000001.10:55529152:C:C 250938/250948, NC_000001.10:55529152:C:T 10/250948)

- Jul 12, 2019 (153)
26 gnomAD - Exomes

Submission ignored due to conflicting rows:
Row 544313 (NC_000001.10:55529152:C:C 250944/250948, NC_000001.10:55529152:C:G 4/250948)
Row 544314 (NC_000001.10:55529152:C:C 250938/250948, NC_000001.10:55529152:C:T 10/250948)

- Jul 12, 2019 (153)
27 GO Exome Sequencing Project NC_000001.10 - 55529153 Oct 11, 2018 (152)
28 KOREAN population from KRGDB NC_000001.10 - 55529153 Apr 25, 2020 (154)
29 Korean Genome Project NC_000001.11 - 55063480 Apr 25, 2020 (154)
30 The PAGE Study NC_000001.11 - 55063480 Jul 12, 2019 (153)
31 8.3KJPN NC_000001.10 - 55529153 Apr 25, 2021 (155)
32 TopMed NC_000001.11 - 55063480 Apr 25, 2021 (155)
33 ALFA NC_000001.11 - 55063480 Apr 25, 2021 (155)
34 ClinVar RCV001186682.1 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
1036631, 1925147, ss1685565556, ss2731525782, ss3893859237, ss5143955840 NC_000001.10:55529152:C:G NC_000001.11:55063479:C:G (self)
892968, ss3944514967 NC_000001.11:55063479:C:G NC_000001.11:55063479:C:G (self)
1614589, 74089, ss341966602, ss488669567, ss1290896042, ss1685565555, ss1958273616, ss2324752166, ss2731525782, ss2746340040, ss2755162395, ss3021088399, ss3651414867, ss3823615423 NC_000001.10:55529152:C:T NC_000001.11:55063479:C:T (self)
RCV001186682.1, 11425239, 30800, 13377322, 1622337042, ss3076677158, ss3725025168, ss3770809331, ss4449770987 NC_000001.11:55063479:C:T NC_000001.11:55063479: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 rs147182054

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