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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.

rs149139428

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:55052746 (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>C
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.000042 (11/264690, TOPMED)
A=0.000031 (5/163746, ALFA)
A=0.000029 (4/140296, GnomAD) (+ 2 more)
A=0.000025 (3/118816, ExAC)
A=0.00015 (2/13006, GO-ESP)
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.55052746G>A
GRCh38.p13 chr 1 NC_000001.11:g.55052746G>C
GRCh37.p13 chr 1 NC_000001.10:g.55518419G>A
GRCh37.p13 chr 1 NC_000001.10:g.55518419G>C
PCSK9 RefSeqGene (LRG_275) NG_009061.1:g.18200G>A
PCSK9 RefSeqGene (LRG_275) NG_009061.1:g.18200G>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.754G>A V [GTG] > M [ATG] Coding Sequence Variant
proprotein convertase subtilisin/kexin type 9 preproprotein NP_777596.2:p.Val252Met V (Val) > M (Met) Missense Variant
PCSK9 transcript variant 1 NM_174936.4:c.754G>C V [GTG] > L [CTG] Coding Sequence Variant
proprotein convertase subtilisin/kexin type 9 preproprotein NP_777596.2:p.Val252Leu V (Val) > L (Leu) Missense Variant
PCSK9 transcript variant 2 NR_110451.2:n.413G>A N/A Non Coding Transcript Variant
PCSK9 transcript variant 2 NR_110451.2:n.413G>C 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: A (allele ID: 907370 )
ClinVar Accession Disease Names Clinical Significance
RCV001179830.1 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 163746 G=0.999969 A=0.000031
European Sub 146838 G=0.999980 A=0.000020
African Sub 4290 G=1.0000 A=0.0000
African Others Sub 168 G=1.000 A=0.000
African American Sub 4122 G=1.0000 A=0.0000
Asian Sub 3338 G=1.0000 A=0.0000
East Asian Sub 2686 G=1.0000 A=0.0000
Other Asian Sub 652 G=1.000 A=0.000
Latin American 1 Sub 442 G=1.000 A=0.000
Latin American 2 Sub 950 G=1.000 A=0.000
South Asian Sub 280 G=1.000 A=0.000
Other Sub 7608 G=0.9997 A=0.0003


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=0.999958 A=0.000042
gnomAD - Genomes Global Study-wide 140296 G=0.999971 A=0.000029
gnomAD - Genomes European Sub 75956 G=0.99997 A=0.00003
gnomAD - Genomes African Sub 42062 G=0.99995 A=0.00005
gnomAD - Genomes American Sub 13666 G=1.00000 A=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3324 G=1.0000 A=0.0000
gnomAD - Genomes East Asian Sub 3134 G=1.0000 A=0.0000
gnomAD - Genomes Other Sub 2154 G=1.0000 A=0.0000
ExAC Global Study-wide 118816 G=0.999975 A=0.000025
ExAC Europe Sub 71324 G=0.99999 A=0.00001
ExAC Asian Sub 25074 G=1.00000 A=0.00000
ExAC American Sub 11494 G=1.00000 A=0.00000
ExAC African Sub 10040 G=0.99980 A=0.00020
ExAC Other Sub 884 G=1.000 A=0.000
GO Exome Sequencing Project Global Study-wide 13006 G=0.99985 A=0.00015
GO Exome Sequencing Project European American Sub 8600 G=1.0000 A=0.0000
GO Exome Sequencing Project African American Sub 4406 G=0.9995 A=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 G= A C
GRCh38.p13 chr 1 NC_000001.11:g.55052746= NC_000001.11:g.55052746G>A NC_000001.11:g.55052746G>C
GRCh37.p13 chr 1 NC_000001.10:g.55518419= NC_000001.10:g.55518419G>A NC_000001.10:g.55518419G>C
PCSK9 RefSeqGene (LRG_275) NG_009061.1:g.18200= NG_009061.1:g.18200G>A NG_009061.1:g.18200G>C
PCSK9 transcript variant 1 NM_174936.4:c.754= NM_174936.4:c.754G>A NM_174936.4:c.754G>C
PCSK9 transcript variant 1 NM_174936.3:c.754= NM_174936.3:c.754G>A NM_174936.3:c.754G>C
PCSK9 transcript variant 2 NR_110451.2:n.413= NR_110451.2:n.413G>A NR_110451.2:n.413G>C
PCSK9 transcript variant 2 NR_110451.1:n.413= NR_110451.1:n.413G>A NR_110451.1:n.413G>C
proprotein convertase subtilisin/kexin type 9 preproprotein NP_777596.2:p.Val252= NP_777596.2:p.Val252Met NP_777596.2:p.Val252Leu
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#.

26 SubSNP, 7 Frequency, 1 ClinVar submissions
No Submitter Submission ID Date (Build)
1 NHLBI-ESP ss341966506 May 09, 2011 (134)
2 EXOME_CHIP ss491294414 May 04, 2012 (137)
3 ILLUMINA ss780860215 Sep 08, 2015 (146)
4 ILLUMINA ss783544622 Sep 08, 2015 (146)
5 EVA_EXAC ss1685565191 Apr 01, 2015 (144)
6 ILLUMINA ss1751925303 Sep 08, 2015 (146)
7 ILLUMINA ss1917729178 Feb 12, 2016 (147)
8 ILLUMINA ss1945995586 Feb 12, 2016 (147)
9 ILLUMINA ss1958273554 Feb 12, 2016 (147)
10 GNOMAD ss2746339848 Nov 08, 2017 (151)
11 GNOMAD ss2755161463 Nov 08, 2017 (151)
12 AFFY ss2984860005 Nov 08, 2017 (151)
13 ILLUMINA ss3021088330 Nov 08, 2017 (151)
14 TOPMED ss3076675024 Nov 08, 2017 (151)
15 ILLUMINA ss3626098043 Oct 11, 2018 (152)
16 ILLUMINA ss3634324673 Oct 11, 2018 (152)
17 ILLUMINA ss3640032034 Oct 11, 2018 (152)
18 ILLUMINA ss3644491501 Oct 11, 2018 (152)
19 ILLUMINA ss3651414776 Oct 11, 2018 (152)
20 ILLUMINA ss3653632522 Oct 11, 2018 (152)
21 ILLUMINA ss3725025113 Jul 12, 2019 (153)
22 ILLUMINA ss3744346081 Jul 12, 2019 (153)
23 ILLUMINA ss3744625594 Jul 12, 2019 (153)
24 ILLUMINA ss3772127016 Jul 12, 2019 (153)
25 EVA ss3823615328 Apr 25, 2020 (154)
26 TOPMED ss4449768161 Apr 25, 2021 (155)
27 ExAC NC_000001.10 - 55518419 Oct 11, 2018 (152)
28 gnomAD - Genomes NC_000001.11 - 55052746 Apr 25, 2021 (155)
29 gnomAD - Exomes

Submission ignored due to conflicting rows:
Row 543728 (NC_000001.10:55518418:G:G 248899/248904, NC_000001.10:55518418:G:A 5/248904)
Row 543729 (NC_000001.10:55518418:G:G 248903/248904, NC_000001.10:55518418:G:C 1/248904)

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

Submission ignored due to conflicting rows:
Row 543728 (NC_000001.10:55518418:G:G 248899/248904, NC_000001.10:55518418:G:A 5/248904)
Row 543729 (NC_000001.10:55518418:G:G 248903/248904, NC_000001.10:55518418:G:C 1/248904)

- Jul 12, 2019 (153)
31 GO Exome Sequencing Project NC_000001.10 - 55518419 Oct 11, 2018 (152)
32 TopMed NC_000001.11 - 55052746 Apr 25, 2021 (155)
33 ALFA NC_000001.11 - 55052746 Apr 25, 2021 (155)
34 ClinVar RCV001179830.1 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
4763239, 73995, ss341966506, ss491294414, ss780860215, ss783544622, ss1685565191, ss1751925303, ss1917729178, ss1945995586, ss1958273554, ss2746339848, ss2755161463, ss2984860005, ss3021088330, ss3626098043, ss3634324673, ss3640032034, ss3644491501, ss3651414776, ss3653632522, ss3744346081, ss3744625594, ss3772127016, ss3823615328 NC_000001.10:55518418:G:A NC_000001.11:55052745:G:A (self)
RCV001179830.1, 11422908, 8417591, 13374496, 7235239825, ss3076675024, ss3725025113, ss4449768161 NC_000001.11:55052745:G:A NC_000001.11:55052745:G:A (self)
NC_000001.10:55518418:G:C NC_000001.11:55052745:G:C (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 rs149139428

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