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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.

rs45613943

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:55052949 (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
T>C
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.123843 (32780/264690, TOPMED)
C=0.116054 (16255/140064, GnomAD)
C=0.08491 (1604/18890, ALFA) (+ 12 more)
C=0.02220 (372/16760, 8.3KJPN)
C=0.1224 (613/5008, 1000G)
C=0.0324 (145/4480, Estonian)
C=0.0503 (194/3854, ALSPAC)
C=0.0534 (198/3708, TWINSUK)
C=0.0281 (82/2922, KOREAN)
C=0.047 (47/998, GoNL)
C=0.055 (33/600, NorthernSweden)
C=0.213 (46/216, Qatari)
T=0.436 (48/110, SGDP_PRJ)
C=0.03 (1/40, GENOME_DK)
T=0.3 (2/6, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
PCSK9 : Intron Variant
Publications
1 citation
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.55052949T>C
GRCh37.p13 chr 1 NC_000001.10:g.55518622T>C
PCSK9 RefSeqGene (LRG_275) NG_009061.1:g.18403T>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.799+158T>C 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.

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 18890 T=0.91509 C=0.08491
European Sub 14286 T=0.95142 C=0.04858
African Sub 2946 T=0.7332 C=0.2668
African Others Sub 114 T=0.772 C=0.228
African American Sub 2832 T=0.7316 C=0.2684
Asian Sub 112 T=0.964 C=0.036
East Asian Sub 86 T=0.97 C=0.03
Other Asian Sub 26 T=0.96 C=0.04
Latin American 1 Sub 146 T=0.884 C=0.116
Latin American 2 Sub 610 T=0.941 C=0.059
South Asian Sub 98 T=0.90 C=0.10
Other Sub 692 T=0.918 C=0.082


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 T=0.876157 C=0.123843
gnomAD - Genomes Global Study-wide 140064 T=0.883946 C=0.116054
gnomAD - Genomes European Sub 75892 T=0.95430 C=0.04570
gnomAD - Genomes African Sub 41920 T=0.73220 C=0.26780
gnomAD - Genomes American Sub 13648 T=0.93501 C=0.06499
gnomAD - Genomes Ashkenazi Jewish Sub 3320 T=0.8967 C=0.1033
gnomAD - Genomes East Asian Sub 3130 T=0.9642 C=0.0358
gnomAD - Genomes Other Sub 2154 T=0.8983 C=0.1017
8.3KJPN JAPANESE Study-wide 16760 T=0.97780 C=0.02220
1000Genomes Global Study-wide 5008 T=0.8776 C=0.1224
1000Genomes African Sub 1322 T=0.7133 C=0.2867
1000Genomes East Asian Sub 1008 T=0.9722 C=0.0278
1000Genomes Europe Sub 1006 T=0.9414 C=0.0586
1000Genomes South Asian Sub 978 T=0.898 C=0.102
1000Genomes American Sub 694 T=0.932 C=0.068
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.9676 C=0.0324
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.9497 C=0.0503
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.9466 C=0.0534
KOREAN population from KRGDB KOREAN Study-wide 2922 T=0.9719 C=0.0281
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 T=0.953 C=0.047
Northern Sweden ACPOP Study-wide 600 T=0.945 C=0.055
Qatari Global Study-wide 216 T=0.787 C=0.213
SGDP_PRJ Global Study-wide 110 T=0.436 C=0.564
The Danish reference pan genome Danish Study-wide 40 T=0.97 C=0.03
Siberian Global Study-wide 6 T=0.3 C=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 T= C
GRCh38.p13 chr 1 NC_000001.11:g.55052949= NC_000001.11:g.55052949T>C
GRCh37.p13 chr 1 NC_000001.10:g.55518622= NC_000001.10:g.55518622T>C
PCSK9 RefSeqGene (LRG_275) NG_009061.1:g.18403= NG_009061.1:g.18403T>C
PCSK9 transcript variant 1 NM_174936.3:c.799+158= NM_174936.3:c.799+158T>C
PCSK9 transcript variant 1 NM_174936.4:c.799+158= NM_174936.4:c.799+158T>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#.

43 SubSNP, 15 Frequency submissions
No Submitter Submission ID Date (Build)
1 PGA-UW-FHCRC ss69358645 May 18, 2007 (127)
2 ILLUMINA-UK ss118698328 Feb 14, 2009 (130)
3 BUSHMAN ss198458395 Jul 04, 2010 (132)
4 1000GENOMES ss210526306 Jul 14, 2010 (132)
5 1000GENOMES ss218385346 Jul 14, 2010 (132)
6 1000GENOMES ss230534741 Jul 14, 2010 (132)
7 GMI ss275826980 May 04, 2012 (137)
8 TISHKOFF ss554113707 Apr 25, 2013 (138)
9 SSMP ss647944650 Apr 25, 2013 (138)
10 EVA-GONL ss975161004 Aug 21, 2014 (142)
11 1000GENOMES ss1290895699 Aug 21, 2014 (142)
12 DDI ss1425808439 Apr 01, 2015 (144)
13 EVA_GENOME_DK ss1574059304 Apr 01, 2015 (144)
14 EVA_DECODE ss1584527339 Apr 01, 2015 (144)
15 EVA_UK10K_ALSPAC ss1600174853 Apr 01, 2015 (144)
16 EVA_UK10K_TWINSUK ss1643168886 Apr 01, 2015 (144)
17 HAMMER_LAB ss1794365809 Sep 08, 2015 (146)
18 WEILL_CORNELL_DGM ss1918369831 Feb 12, 2016 (147)
19 JJLAB ss2019700514 Sep 14, 2016 (149)
20 USC_VALOUEV ss2147714850 Dec 20, 2016 (150)
21 HUMAN_LONGEVITY ss2162511149 Dec 20, 2016 (150)
22 TOPMED ss2324751454 Dec 20, 2016 (150)
23 GRF ss2697627263 Nov 08, 2017 (151)
24 GNOMAD ss2755161485 Nov 08, 2017 (151)
25 SWEGEN ss2986819026 Nov 08, 2017 (151)
26 BIOINF_KMB_FNS_UNIBA ss3023610322 Nov 08, 2017 (151)
27 TOPMED ss3076675068 Nov 08, 2017 (151)
28 CSHL ss3343453952 Nov 08, 2017 (151)
29 EGCUT_WGS ss3654882628 Jul 12, 2019 (153)
30 EVA_DECODE ss3686773673 Jul 12, 2019 (153)
31 ACPOP ss3727047711 Jul 12, 2019 (153)
32 EVA ss3746204758 Jul 12, 2019 (153)
33 PACBIO ss3783409031 Jul 12, 2019 (153)
34 PACBIO ss3789067006 Jul 12, 2019 (153)
35 PACBIO ss3793939703 Jul 12, 2019 (153)
36 KHV_HUMAN_GENOMES ss3799214032 Jul 12, 2019 (153)
37 EVA ss3826172026 Apr 25, 2020 (154)
38 EVA ss3836472668 Apr 25, 2020 (154)
39 EVA ss3841878737 Apr 25, 2020 (154)
40 SGDP_PRJ ss3848848290 Apr 25, 2020 (154)
41 KRGDB ss3893859054 Apr 25, 2020 (154)
42 TOPMED ss4449768220 Apr 25, 2021 (155)
43 TOMMO_GENOMICS ss5143955485 Apr 25, 2021 (155)
44 1000Genomes NC_000001.10 - 55518622 Oct 11, 2018 (152)
45 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 55518622 Oct 11, 2018 (152)
46 Genetic variation in the Estonian population NC_000001.10 - 55518622 Oct 11, 2018 (152)
47 The Danish reference pan genome NC_000001.10 - 55518622 Apr 25, 2020 (154)
48 gnomAD - Genomes NC_000001.11 - 55052949 Apr 25, 2021 (155)
49 Genome of the Netherlands Release 5 NC_000001.10 - 55518622 Apr 25, 2020 (154)
50 KOREAN population from KRGDB NC_000001.10 - 55518622 Apr 25, 2020 (154)
51 Northern Sweden NC_000001.10 - 55518622 Jul 12, 2019 (153)
52 Qatari NC_000001.10 - 55518622 Apr 25, 2020 (154)
53 SGDP_PRJ NC_000001.10 - 55518622 Apr 25, 2020 (154)
54 Siberian NC_000001.10 - 55518622 Apr 25, 2020 (154)
55 8.3KJPN NC_000001.10 - 55518622 Apr 25, 2021 (155)
56 TopMed NC_000001.11 - 55052949 Apr 25, 2021 (155)
57 UK 10K study - Twins NC_000001.10 - 55518622 Oct 11, 2018 (152)
58 ALFA NC_000001.11 - 55052949 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
ss118698328, ss198458395, ss210526306, ss275826980, ss1584527339 NC_000001.9:55291209:T:C NC_000001.11:55052948:T:C (self)
1614237, 878048, 620876, 1501784, 372386, 1036448, 332576, 411761, 865270, 231204, 1924792, 878048, ss218385346, ss230534741, ss554113707, ss647944650, ss975161004, ss1290895699, ss1425808439, ss1574059304, ss1600174853, ss1643168886, ss1794365809, ss1918369831, ss2019700514, ss2147714850, ss2324751454, ss2697627263, ss2755161485, ss2986819026, ss3343453952, ss3654882628, ss3727047711, ss3746204758, ss3783409031, ss3789067006, ss3793939703, ss3826172026, ss3836472668, ss3848848290, ss3893859054, ss5143955485 NC_000001.10:55518621:T:C NC_000001.11:55052948:T:C (self)
11422964, 8417631, 13374555, 10770539523, ss2162511149, ss3023610322, ss3076675068, ss3686773673, ss3799214032, ss3841878737, ss4449768220 NC_000001.11:55052948:T:C NC_000001.11:55052948:T:C (self)
ss69358645 NT_032977.9:25490539:T:C NC_000001.11:55052948:T:C (self)
Help

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

1 citation for rs45613943
PMID Title Author Year Journal
32084179 Genetic associations between serum low LDL-cholesterol levels and variants in LDLR, APOB, PCSK9 and LDLRAP1 in African populations. Hayat M et al. 2020 PloS one
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