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dbSNP Short Genetic Variations

Examples: rs268, BRCA1 and more Advanced search

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.

rs5126

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr19:44949172 (GRCh38.p14) 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
A>C
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.008255 (2185/264690, TOPMED)
C=0.001828 (459/251064, GnomAD_exome)
C=0.000770 (154/199894, ALFA) (+ 9 more)
C=0.007841 (1098/140036, GnomAD)
C=0.002375 (276/116204, ExAC)
C=0.01219 (959/78702, PAGE_STUDY)
C=0.0089 (57/6404, 1000G_30x)
C=0.0078 (39/5008, 1000G)
C=0.021 (7/328, HapMap)
C=0.009 (2/216, Qatari)
A=0.5 (1/2, SGDP_PRJ)
C=0.5 (1/2, SGDP_PRJ)
Clinical Significance
Reported in ClinVar
Gene : Consequence
APOC2 : Missense Variant
APOC4-APOC2 : Non Coding Transcript Variant
Publications
1 citation
Genomic View
See rs on genome

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: 20231103111315
Population Group Sample Size Ref Allele Alt Allele Ref HMOZ Alt HMOZ HTRZ HWEP
Total Global 216304 A=0.998659 C=0.001341 0.997346 2.8e-05 0.002626 22
European Sub 178160 A=0.999961 C=0.000039 0.999921 0.0 0.000079 0
African Sub 10090 A=0.97502 C=0.02498 0.950644 0.000595 0.048761 0
African Others Sub 358 A=0.980 C=0.020 0.960894 0.0 0.039106 0
African American Sub 9732 A=0.9748 C=0.0252 0.950267 0.000617 0.049116 0
Asian Sub 6372 A=1.0000 C=0.0000 1.0 0.0 0.0 N/A
East Asian Sub 4520 A=1.0000 C=0.0000 1.0 0.0 0.0 N/A
Other Asian Sub 1852 A=1.0000 C=0.0000 1.0 0.0 0.0 N/A
Latin American 1 Sub 810 A=0.995 C=0.005 0.990123 0.0 0.009877 0
Latin American 2 Sub 1002 A=0.9980 C=0.0020 0.996008 0.0 0.003992 0
South Asian Sub 296 A=1.000 C=0.000 1.0 0.0 0.0 N/A
Other Sub 19574 A=0.99872 C=0.00128 0.997446 0.0 0.002554 0


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 A=0.991745 C=0.008255
gnomAD - Exomes Global Study-wide 251064 A=0.998172 C=0.001828
gnomAD - Exomes European Sub 135272 A=0.999956 C=0.000044
gnomAD - Exomes Asian Sub 48966 A=0.99998 C=0.00002
gnomAD - Exomes American Sub 34500 A=0.99919 C=0.00081
gnomAD - Exomes African Sub 16142 A=0.97392 C=0.02608
gnomAD - Exomes Ashkenazi Jewish Sub 10056 A=1.00000 C=0.00000
gnomAD - Exomes Other Sub 6128 A=0.9995 C=0.0005
Allele Frequency Aggregator Total Global 199894 A=0.999230 C=0.000770
Allele Frequency Aggregator European Sub 168022 A=0.999958 C=0.000042
Allele Frequency Aggregator Other Sub 18140 A=0.99906 C=0.00094
Allele Frequency Aggregator Asian Sub 6372 A=1.0000 C=0.0000
Allele Frequency Aggregator African Sub 5252 A=0.9764 C=0.0236
Allele Frequency Aggregator Latin American 2 Sub 1002 A=0.9980 C=0.0020
Allele Frequency Aggregator Latin American 1 Sub 810 A=0.995 C=0.005
Allele Frequency Aggregator South Asian Sub 296 A=1.000 C=0.000
gnomAD - Genomes Global Study-wide 140036 A=0.992159 C=0.007841
gnomAD - Genomes European Sub 75878 A=0.99992 C=0.00008
gnomAD - Genomes African Sub 41930 A=0.97482 C=0.02518
gnomAD - Genomes American Sub 13630 A=0.99831 C=0.00169
gnomAD - Genomes Ashkenazi Jewish Sub 3324 A=1.0000 C=0.0000
gnomAD - Genomes East Asian Sub 3124 A=1.0000 C=0.0000
gnomAD - Genomes Other Sub 2150 A=0.9940 C=0.0060
ExAC Global Study-wide 116204 A=0.997625 C=0.002375
ExAC Europe Sub 70794 A=0.99996 C=0.00004
ExAC Asian Sub 24288 A=1.00000 C=0.00000
ExAC American Sub 10790 A=0.99917 C=0.00083
ExAC African Sub 9464 A=0.9721 C=0.0279
ExAC Other Sub 868 A=1.000 C=0.000
The PAGE Study Global Study-wide 78702 A=0.98781 C=0.01219
The PAGE Study AfricanAmerican Sub 32516 A=0.97389 C=0.02611
The PAGE Study Mexican Sub 10810 A=0.99880 C=0.00120
The PAGE Study Asian Sub 8318 A=1.0000 C=0.0000
The PAGE Study PuertoRican Sub 7918 A=0.9961 C=0.0039
The PAGE Study NativeHawaiian Sub 4534 A=1.0000 C=0.0000
The PAGE Study Cuban Sub 4230 A=0.9974 C=0.0026
The PAGE Study Dominican Sub 3828 A=0.9901 C=0.0099
The PAGE Study CentralAmerican Sub 2450 A=0.9967 C=0.0033
The PAGE Study SouthAmerican Sub 1982 A=0.9980 C=0.0020
The PAGE Study NativeAmerican Sub 1260 A=0.9960 C=0.0040
The PAGE Study SouthAsian Sub 856 A=1.000 C=0.000
1000Genomes_30x Global Study-wide 6404 A=0.9911 C=0.0089
1000Genomes_30x African Sub 1786 A=0.9692 C=0.0308
1000Genomes_30x Europe Sub 1266 A=1.0000 C=0.0000
1000Genomes_30x South Asian Sub 1202 A=1.0000 C=0.0000
1000Genomes_30x East Asian Sub 1170 A=1.0000 C=0.0000
1000Genomes_30x American Sub 980 A=0.998 C=0.002
1000Genomes Global Study-wide 5008 A=0.9922 C=0.0078
1000Genomes African Sub 1322 A=0.9713 C=0.0287
1000Genomes East Asian Sub 1008 A=1.0000 C=0.0000
1000Genomes Europe Sub 1006 A=1.0000 C=0.0000
1000Genomes South Asian Sub 978 A=1.000 C=0.000
1000Genomes American Sub 694 A=0.999 C=0.001
HapMap Global Study-wide 328 A=0.979 C=0.021
HapMap African Sub 120 A=0.942 C=0.058
HapMap American Sub 120 A=1.000 C=0.000
HapMap Asian Sub 88 A=1.00 C=0.00
Qatari Global Study-wide 216 A=0.991 C=0.009
SGDP_PRJ Global Study-wide 2 A=0.5 C=0.5
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.p14 chr 19 NC_000019.10:g.44949172A>C
GRCh37.p13 chr 19 NC_000019.9:g.45452429A>C
APOC2 RefSeqGene NG_008837.1:g.8187A>C
Gene: APOC2, apolipoprotein C2 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
APOC2 transcript NM_000483.5:c.229A>C K [AAA] > Q [CAA] Coding Sequence Variant
apolipoprotein C-II precursor NP_000474.2:p.Lys77Gln K (Lys) > Q (Gln) Missense Variant
Gene: APOC4-APOC2, APOC4-APOC2 readthrough (NMD candidate) (plus strand)
Molecule type Change Amino acid[Codon] SO Term
APOC4-APOC2 transcript NR_037932.1:n.1436A>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: C (allele ID: 17612 )
ClinVar Accession Disease Names Clinical Significance
RCV000002682.2 APOLIPOPROTEIN C-II (AFRICAN) Pathogenic
RCV000974450.7 not provided Benign-Likely-Benign
RCV000991188.3 Familial apolipoprotein C-II deficiency Benign
RCV001777130.1 not specified Benign
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 A= C
GRCh38.p14 chr 19 NC_000019.10:g.44949172= NC_000019.10:g.44949172A>C
GRCh37.p13 chr 19 NC_000019.9:g.45452429= NC_000019.9:g.45452429A>C
APOC2 RefSeqGene NG_008837.1:g.8187= NG_008837.1:g.8187A>C
APOC2 transcript NM_000483.5:c.229= NM_000483.5:c.229A>C
APOC2 transcript NM_000483.4:c.229= NM_000483.4:c.229A>C
APOC4-APOC2 transcript NR_037932.1:n.1436= NR_037932.1:n.1436A>C
apolipoprotein C-II precursor NP_000474.2:p.Lys77= NP_000474.2:p.Lys77Gln
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#.

62 SubSNP, 11 Frequency, 4 ClinVar submissions
No Submitter Submission ID Date (Build)
1 ARAVINDA ss6570 Sep 19, 2000 (52)
2 PERLEGEN ss69229174 May 17, 2007 (127)
3 AFFY ss74815052 Aug 16, 2007 (128)
4 1000GENOMES ss115184974 Jan 25, 2009 (130)
5 SEATTLESEQ ss159740190 Dec 01, 2009 (131)
6 ILLUMINA ss161064112 Dec 01, 2009 (131)
7 COMPLETE_GENOMICS ss169834665 Jul 04, 2010 (132)
8 ILLUMINA ss244302817 Jul 04, 2010 (132)
9 OMIM-CURATED-RECORDS ss255603822 Aug 20, 2010 (132)
10 1000GENOMES ss340491500 May 09, 2011 (134)
11 NHLBI-ESP ss342502275 May 09, 2011 (134)
12 ILLUMINA ss410938459 Sep 17, 2011 (135)
13 ILLUMINA ss479284123 Sep 08, 2015 (146)
14 1000GENOMES ss491161778 May 04, 2012 (137)
15 EXOME_CHIP ss491549573 May 04, 2012 (137)
16 CLINSEQ_SNP ss491769750 May 04, 2012 (137)
17 ILLUMINA ss534595204 Sep 08, 2015 (146)
18 ILLUMINA ss780747112 Sep 08, 2015 (146)
19 ILLUMINA ss783424875 Sep 08, 2015 (146)
20 1000GENOMES ss1363327459 Aug 21, 2014 (142)
21 EVA_EXAC ss1693665925 Apr 01, 2015 (144)
22 ILLUMINA ss1752288255 Sep 08, 2015 (146)
23 ILLUMINA ss1917938940 Feb 12, 2016 (147)
24 WEILL_CORNELL_DGM ss1937836187 Feb 12, 2016 (147)
25 ILLUMINA ss1946537680 Feb 12, 2016 (147)
26 ILLUMINA ss1959869775 Feb 12, 2016 (147)
27 HUMAN_LONGEVITY ss2226014783 Dec 20, 2016 (150)
28 GNOMAD ss2744091439 Nov 08, 2017 (151)
29 GNOMAD ss2750219121 Nov 08, 2017 (151)
30 GNOMAD ss2963334193 Nov 08, 2017 (151)
31 AFFY ss2985144709 Nov 08, 2017 (151)
32 ILLUMINA ss3021911704 Nov 08, 2017 (151)
33 ILLUMINA ss3627941700 Oct 12, 2018 (152)
34 ILLUMINA ss3627941701 Oct 12, 2018 (152)
35 ILLUMINA ss3634738136 Oct 12, 2018 (152)
36 ILLUMINA ss3636425186 Oct 12, 2018 (152)
37 ILLUMINA ss3640445444 Oct 12, 2018 (152)
38 ILLUMINA ss3644726195 Oct 12, 2018 (152)
39 ILLUMINA ss3652337816 Oct 12, 2018 (152)
40 ILLUMINA ss3653917456 Oct 12, 2018 (152)
41 ILLUMINA ss3725733676 Jul 13, 2019 (153)
42 ILLUMINA ss3744466163 Jul 13, 2019 (153)
43 ILLUMINA ss3745038145 Jul 13, 2019 (153)
44 PAGE_CC ss3772017048 Jul 13, 2019 (153)
45 ILLUMINA ss3772535229 Jul 13, 2019 (153)
46 KHV_HUMAN_GENOMES ss3821360277 Jul 13, 2019 (153)
47 EVA ss3825301517 Apr 27, 2020 (154)
48 SGDP_PRJ ss3888306090 Apr 27, 2020 (154)
49 EVA ss3986802326 Apr 26, 2021 (155)
50 TOPMED ss5076176764 Apr 26, 2021 (155)
51 EVA ss5236962753 Apr 26, 2021 (155)
52 1000G_HIGH_COVERAGE ss5307396897 Oct 13, 2022 (156)
53 EVA ss5435089195 Oct 13, 2022 (156)
54 HUGCELL_USP ss5499892525 Oct 13, 2022 (156)
55 1000G_HIGH_COVERAGE ss5613192889 Oct 13, 2022 (156)
56 SANFORD_IMAGENETICS ss5624429791 Oct 13, 2022 (156)
57 SANFORD_IMAGENETICS ss5662476239 Oct 13, 2022 (156)
58 EVA ss5840607196 Oct 13, 2022 (156)
59 EVA ss5847846278 Oct 13, 2022 (156)
60 EVA ss5928257448 Oct 13, 2022 (156)
61 EVA ss5953885959 Oct 13, 2022 (156)
62 EVA ss5979547925 Oct 13, 2022 (156)
63 1000Genomes NC_000019.9 - 45452429 Oct 12, 2018 (152)
64 1000Genomes_30x NC_000019.10 - 44949172 Oct 13, 2022 (156)
65 ExAC NC_000019.9 - 45452429 Oct 12, 2018 (152)
66 gnomAD - Genomes NC_000019.10 - 44949172 Apr 26, 2021 (155)
67 gnomAD - Exomes NC_000019.9 - 45452429 Jul 13, 2019 (153)
68 HapMap NC_000019.10 - 44949172 Apr 27, 2020 (154)
69 The PAGE Study NC_000019.10 - 44949172 Jul 13, 2019 (153)
70 Qatari NC_000019.9 - 45452429 Apr 27, 2020 (154)
71 SGDP_PRJ NC_000019.9 - 45452429 Apr 27, 2020 (154)
72 TopMed NC_000019.10 - 44949172 Apr 26, 2021 (155)
73 ALFA NC_000019.10 - 44949172 Apr 26, 2021 (155)
74 ClinVar RCV000002682.2 Oct 12, 2018 (152)
75 ClinVar RCV000974450.7 Oct 13, 2022 (156)
76 ClinVar RCV000991188.3 Oct 13, 2022 (156)
77 ClinVar RCV001777130.1 Oct 13, 2022 (156)
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).

Associated ID History Updated (Build)
rs52806093 Sep 21, 2007 (128)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss115184974, ss169834665, ss491769750 NC_000019.8:50144268:A:C NC_000019.10:44949171:A:C (self)
76740043, 4174665, 13407186, 19878109, 40323070, ss340491500, ss342502275, ss479284123, ss491161778, ss491549573, ss534595204, ss780747112, ss783424875, ss1363327459, ss1693665925, ss1752288255, ss1917938940, ss1937836187, ss1946537680, ss1959869775, ss2744091439, ss2750219121, ss2963334193, ss2985144709, ss3021911704, ss3627941700, ss3627941701, ss3634738136, ss3636425186, ss3640445444, ss3644726195, ss3652337816, ss3653917456, ss3744466163, ss3745038145, ss3772535229, ss3825301517, ss3888306090, ss3986802326, ss5435089195, ss5624429791, ss5662476239, ss5840607196, ss5847846278, ss5953885959, ss5979547925 NC_000019.9:45452428:A:C NC_000019.10:44949171:A:C (self)
RCV000002682.2, RCV000974450.7, RCV000991188.3, RCV001777130.1, 100718824, 541203043, 1701775, 1238517, 291722428, 2566853307, ss255603822, ss2226014783, ss3725733676, ss3772017048, ss3821360277, ss5076176764, ss5236962753, ss5307396897, ss5499892525, ss5613192889, ss5928257448 NC_000019.10:44949171:A:C NC_000019.10:44949171:A:C (self)
ss6570, ss69229174, ss74815052, ss159740190, ss161064112, ss244302817, ss410938459 NT_011109.16:17720646:A:C NC_000019.10:44949171:A: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 rs5126
PMID Title Author Year Journal
3944271 A variant primary structure of apolipoprotein C-II in individuals of African descent. Menzel HJ et al. 1986 The Journal of clinical investigation
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.post820+afb47a3d