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dbSNP Short Genetic Variations

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.

rs147859257

Current Build 152

Released October 2, 2018

Organism
Homo sapiens
Position
chr19:6718135 (GRCh38.p12) 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>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.00281 (692/246254, GnomAD)
G=0.00252 (316/125568, TOPMED)
G=0.00336 (408/121354, ExAC) (+ 6 more)
G=0.0021 (64/30920, GnomAD)
G=0.0029 (38/13006, GO-ESP)
G=0.000 (2/5008, 1000G)
G=0.002 (8/4480, Estonian)
G=0.007 (26/3854, ALSPAC)
G=0.004 (13/3708, TWINSUK)
Clinical Significance
Reported in ClinVar
Gene : Consequence
C3 : Missense 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.p12 chr 19 NC_000019.10:g.6718135T>G
GRCh37.p13 chr 19 NC_000019.9:g.6718146T>G
C3 RefSeqGene (LRG_27) NG_009557.1:g.7517A>C
Gene: C3, complement C3 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
C3 transcript NM_000064.3:c.463A>C K [AAG] > Q [CAG] Coding Sequence Variant
complement C3 preproprotein NP_000055.2:p.Lys155Gln K (Lys) > Q (Gln) Missense 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: G (allele ID: 97565 )
ClinVar Accession Disease Names Clinical Significance
RCV000077796.4 MACULAR DEGENERATION, AGE-RELATED, 9, SUSCEPTIBILITY TO Risk-Factor
RCV000202831.1 not specified Uncertain-Significance
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 125568 T=0.99748 G=0.00252
ExAC Global Study-wide 121354 T=0.99664 G=0.00336
ExAC Europe Sub 73314 T=0.9946 G=0.0054
ExAC Asian Sub 25166 T=1.0000 G=0.0000
ExAC American Sub 11568 T=0.9995 G=0.0005
ExAC African Sub 10402 T=0.9996 G=0.0004
ExAC Other Sub 904 T=1.00 G=0.00
gnomAD - Genomes Global Study-wide 30920 T=0.9979 G=0.0021
gnomAD - Genomes European Sub 18462 T=0.9969 G=0.0031
gnomAD - Genomes African Sub 8718 T=1.000 G=0.000
gnomAD - Genomes East Asian Sub 1622 T=1.000 G=0.000
gnomAD - Genomes Other Sub 978 T=1.00 G=0.00
gnomAD - Genomes American Sub 838 T=1.00 G=0.00
gnomAD - Genomes Ashkenazi Jewish Sub 302 T=1.00 G=0.00
GO Exome Sequencing Project Global Study-wide 13006 T=0.9971 G=0.0029
GO Exome Sequencing Project European American Sub 8600 T=0.996 G=0.004
GO Exome Sequencing Project African American Sub 4406 T=1.000 G=0.000
1000Genomes Global Study-wide 5008 T=1.000 G=0.000
1000Genomes African Sub 1322 T=1.000 G=0.000
1000Genomes East Asian Sub 1008 T=1.000 G=0.000
1000Genomes Europe Sub 1006 T=0.998 G=0.002
1000Genomes South Asian Sub 978 T=1.00 G=0.00
1000Genomes American Sub 694 T=1.00 G=0.00
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.998 G=0.002
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.993 G=0.007
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.996 G=0.004
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= G Note
GRCh38.p12 chr 19 NC_000019.10:g.6718135T= NC_000019.10:g.6718135T>G
GRCh37.p13 chr 19 NC_000019.9:g.6718146T= NC_000019.9:g.6718146T>G
C3 RefSeqGene (LRG_27) NG_009557.1:g.7517A= NG_009557.1:g.7517A>C
C3 transcript NM_000064.3:c.463A= NM_000064.3:c.463A>C
C3 transcript NM_000064.2:c.463A= NM_000064.2:c.463A>C
complement C3 preproprotein NP_000055.2:p.Lys155= NP_000055.2:p.Lys155Gln
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#.

33 SubSNP, 9 Frequency, 2 ClinVar submissions
No Submitter Submission ID Date (Build)
1 NHLBI-ESP ss342482717 May 09, 2011 (134)
2 1000GENOMES ss489147220 May 04, 2012 (137)
3 EXOME_CHIP ss491537971 May 04, 2012 (137)
4 CLINSEQ_SNP ss491755807 May 04, 2012 (137)
5 ILLUMINA ss780739547 Sep 08, 2015 (146)
6 ILLUMINA ss783416709 Sep 08, 2015 (146)
7 OMIM-CURATED-RECORDS ss947844443 Jan 16, 2014 (138)
8 EVA-GONL ss994056146 Aug 21, 2014 (142)
9 1000GENOMES ss1362235005 Aug 21, 2014 (142)
10 EVA_UK10K_ALSPAC ss1637508656 Apr 01, 2015 (144)
11 EVA_UK10K_TWINSUK ss1680502689 Apr 01, 2015 (144)
12 EVA_EXAC ss1693307698 Apr 01, 2015 (144)
13 EVA_DECODE ss1698117695 Apr 01, 2015 (144)
14 ILLUMINA ss1752298569 Sep 08, 2015 (146)
15 ILLUMINA ss1917930817 Feb 12, 2016 (147)
16 ILLUMINA ss1946525106 Feb 12, 2016 (147)
17 ILLUMINA ss1959834420 Feb 12, 2016 (147)
18 JJLAB ss2029542716 Sep 14, 2016 (149)
19 HUMAN_LONGEVITY ss2224055278 Dec 20, 2016 (150)
20 TOPMED ss2389496283 Dec 20, 2016 (150)
21 GNOMAD ss2743537905 Nov 08, 2017 (151)
22 GNOMAD ss2750041065 Nov 08, 2017 (151)
23 GNOMAD ss2960111286 Nov 08, 2017 (151)
24 AFFY ss2985128014 Nov 08, 2017 (151)
25 SWEGEN ss3017040239 Nov 08, 2017 (151)
26 ILLUMINA ss3021875099 Nov 08, 2017 (151)
27 TOPMED ss3287095566 Nov 08, 2017 (151)
28 ILLUMINA ss3627881334 Oct 12, 2018 (152)
29 ILLUMINA ss3634721265 Oct 12, 2018 (152)
30 ILLUMINA ss3640428573 Oct 12, 2018 (152)
31 ILLUMINA ss3644713936 Oct 12, 2018 (152)
32 ILLUMINA ss3652299245 Oct 12, 2018 (152)
33 ILLUMINA ss3653900887 Oct 12, 2018 (152)
34 1000Genomes NC_000019.9 - 6718146 Oct 12, 2018 (152)
35 The Avon Longitudinal Study of Parents and Children NC_000019.9 - 6718146 Oct 12, 2018 (152)
36 Genetic variation in the Estonian population NC_000019.9 - 6718146 Oct 12, 2018 (152)
37 ExAC NC_000019.9 - 6718146 Oct 12, 2018 (152)
38 gnomAD - Genomes NC_000019.9 - 6718146 Oct 12, 2018 (152)
39 gnomAD - Exomes NC_000019.9 - 6718146 Oct 12, 2018 (152)
40 GO Exome Sequencing Project NC_000019.9 - 6718146 Oct 12, 2018 (152)
41 TopMed NC_000019.10 - 6718135 Oct 12, 2018 (152)
42 UK 10K study - Twins NC_000019.9 - 6718146 Oct 12, 2018 (152)
43 ClinVar RCV000077796.4 Oct 12, 2018 (152)
44 ClinVar RCV000202831.1 Oct 12, 2018 (152)
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
ss491755807, ss1698117695 NC_000019.8:6669145:T= NC_000019.10:6718134:T= (self)
75607654, 41897142, 29620682, 3790784, 93812816, 10101842, 1683696, 41897142, ss342482717, ss489147220, ss491537971, ss780739547, ss783416709, ss994056146, ss1362235005, ss1637508656, ss1680502689, ss1693307698, ss1752298569, ss1917930817, ss1946525106, ss1959834420, ss2029542716, ss2389496283, ss2743537905, ss2750041065, ss2960111286, ss2985128014, ss3017040239, ss3021875099, ss3627881334, ss3634721265, ss3640428573, ss3644713936, ss3652299245, ss3653900887 NC_000019.9:6718145:T= NC_000019.10:6718134:T= (self)
176304028, ss947844443, ss2224055278, ss3287095566 NC_000019.10:6718134:T= NC_000019.10:6718134:T= (self)
ss491755807, ss1698117695 NC_000019.8:6669145:T>G NC_000019.10:6718134:T>G (self)
75607654, 41897142, 29620682, 3790784, 93812816, 10101842, 1683696, 41897142, ss342482717, ss489147220, ss491537971, ss780739547, ss783416709, ss994056146, ss1362235005, ss1637508656, ss1680502689, ss1693307698, ss1752298569, ss1917930817, ss1946525106, ss1959834420, ss2029542716, ss2389496283, ss2743537905, ss2750041065, ss2960111286, ss2985128014, ss3017040239, ss3021875099, ss3627881334, ss3634721265, ss3640428573, ss3644713936, ss3652299245, ss3653900887 NC_000019.9:6718145:T>G NC_000019.10:6718134:T>G (self)
RCV000077796.4, RCV000202831.1, 176304028, ss947844443, ss2224055278, ss3287095566 NC_000019.10:6718134:T>G NC_000019.10:6718134:T>G (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 rs147859257
PMID Title Author Year Journal
24036949 Identification of a rare coding variant in complement 3 associated with age-related macular degeneration. Zhan X et al. 2013 Nature genetics
24036950 A rare nonsynonymous sequence variant in C3 is associated with high risk of age-related macular degeneration. Helgason H et al. 2013 Nature genetics
24036952 Rare variants in CFI, C3 and C9 are associated with high risk of advanced age-related macular degeneration. Seddon JM et al. 2013 Nature genetics

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.post76+b4aec9c