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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.

rs5122

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr19:44948823 (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
G>A
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.002274 (602/264690, TOPMED)
A=0.000482 (121/250930, GnomAD_exome)
A=0.000261 (52/199488, ALFA) (+ 6 more)
A=0.002290 (321/140204, GnomAD)
A=0.000588 (71/120776, ExAC)
A=0.0016 (10/6404, 1000G_30x)
A=0.0012 (6/5008, 1000G)
A=0.006 (3/532, HapMap)
A=0.005 (1/216, Qatari)
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 199610 G=0.999739 A=0.000261 0.999479 0.0 0.000521 0
European Sub 169160 G=0.999988 A=0.000012 0.999976 0.0 0.000024 0
African Sub 6098 G=0.9923 A=0.0077 0.984585 0.0 0.015415 0
African Others Sub 206 G=0.995 A=0.005 0.990291 0.0 0.009709 0
African American Sub 5892 G=0.9922 A=0.0078 0.984386 0.0 0.015614 0
Asian Sub 6320 G=0.9998 A=0.0002 0.999684 0.0 0.000316 0
East Asian Sub 4470 G=0.9998 A=0.0002 0.999553 0.0 0.000447 0
Other Asian Sub 1850 G=1.0000 A=0.0000 1.0 0.0 0.0 N/A
Latin American 1 Sub 776 G=0.999 A=0.001 0.997423 0.0 0.002577 0
Latin American 2 Sub 972 G=1.000 A=0.000 1.0 0.0 0.0 N/A
South Asian Sub 274 G=1.000 A=0.000 1.0 0.0 0.0 N/A
Other Sub 16010 G=0.99994 A=0.00006 0.999875 0.0 0.000125 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 G=0.997726 A=0.002274
gnomAD - Exomes Global Study-wide 250930 G=0.999518 A=0.000482
gnomAD - Exomes European Sub 134960 G=0.999985 A=0.000015
gnomAD - Exomes Asian Sub 48964 G=1.00000 A=0.00000
gnomAD - Exomes American Sub 34568 G=0.99968 A=0.00032
gnomAD - Exomes African Sub 16224 G=0.99334 A=0.00666
gnomAD - Exomes Ashkenazi Jewish Sub 10080 G=1.00000 A=0.00000
gnomAD - Exomes Other Sub 6134 G=1.0000 A=0.0000
Allele Frequency Aggregator Total Global 199488 G=0.999739 A=0.000261
Allele Frequency Aggregator European Sub 169056 G=0.999988 A=0.000012
Allele Frequency Aggregator Other Sub 16006 G=0.99994 A=0.00006
Allele Frequency Aggregator Asian Sub 6320 G=0.9998 A=0.0002
Allele Frequency Aggregator African Sub 6084 G=0.9923 A=0.0077
Allele Frequency Aggregator Latin American 2 Sub 972 G=1.000 A=0.000
Allele Frequency Aggregator Latin American 1 Sub 776 G=0.999 A=0.001
Allele Frequency Aggregator South Asian Sub 274 G=1.000 A=0.000
gnomAD - Genomes Global Study-wide 140204 G=0.997710 A=0.002290
gnomAD - Genomes European Sub 75934 G=1.00000 A=0.00000
gnomAD - Genomes African Sub 42014 G=0.99262 A=0.00738
gnomAD - Genomes American Sub 13648 G=0.99949 A=0.00051
gnomAD - Genomes Ashkenazi Jewish Sub 3320 G=1.0000 A=0.0000
gnomAD - Genomes East Asian Sub 3134 G=1.0000 A=0.0000
gnomAD - Genomes Other Sub 2154 G=0.9981 A=0.0019
ExAC Global Study-wide 120776 G=0.999412 A=0.000588
ExAC Europe Sub 73016 G=0.99997 A=0.00003
ExAC Asian Sub 25030 G=1.00000 A=0.00000
ExAC American Sub 11530 G=0.99957 A=0.00043
ExAC African Sub 10294 G=0.99378 A=0.00622
ExAC Other Sub 906 G=1.000 A=0.000
1000Genomes_30x Global Study-wide 6404 G=0.9984 A=0.0016
1000Genomes_30x African Sub 1786 G=0.9955 A=0.0045
1000Genomes_30x Europe Sub 1266 G=1.0000 A=0.0000
1000Genomes_30x South Asian Sub 1202 G=1.0000 A=0.0000
1000Genomes_30x East Asian Sub 1170 G=1.0000 A=0.0000
1000Genomes_30x American Sub 980 G=0.998 A=0.002
1000Genomes Global Study-wide 5008 G=0.9988 A=0.0012
1000Genomes African Sub 1322 G=0.9962 A=0.0038
1000Genomes East Asian Sub 1008 G=1.0000 A=0.0000
1000Genomes Europe Sub 1006 G=1.0000 A=0.0000
1000Genomes South Asian Sub 978 G=1.000 A=0.000
1000Genomes American Sub 694 G=0.999 A=0.001
HapMap Global Study-wide 532 G=0.994 A=0.006
HapMap African Sub 226 G=0.996 A=0.004
HapMap American Sub 218 G=0.991 A=0.009
HapMap Asian Sub 88 G=1.00 A=0.00
Qatari Global Study-wide 216 G=0.995 A=0.005
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.44948823G>A
GRCh37.p13 chr 19 NC_000019.9:g.45452080G>A
APOC2 RefSeqGene NG_008837.1:g.7838G>A
Gene: APOC2, apolipoprotein C2 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
APOC2 transcript NM_000483.5:c.178G>A E [GAG] > K [AAG] Coding Sequence Variant
apolipoprotein C-II precursor NP_000474.2:p.Glu60Lys E (Glu) > K (Lys) 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.1385G>A 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: 17621 )
ClinVar Accession Disease Names Clinical Significance
RCV000002698.2 APOLIPOPROTEIN C-II (SAN FRANCISCO) Pathogenic
RCV000991187.1 Familial apolipoprotein C-II deficiency Uncertain-Significance
RCV001513190.6 not provided Benign-Likely-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 G= A
GRCh38.p14 chr 19 NC_000019.10:g.44948823= NC_000019.10:g.44948823G>A
GRCh37.p13 chr 19 NC_000019.9:g.45452080= NC_000019.9:g.45452080G>A
APOC2 RefSeqGene NG_008837.1:g.7838= NG_008837.1:g.7838G>A
APOC2 transcript NM_000483.5:c.178= NM_000483.5:c.178G>A
APOC2 transcript NM_000483.4:c.178= NM_000483.4:c.178G>A
APOC4-APOC2 transcript NR_037932.1:n.1385= NR_037932.1:n.1385G>A
apolipoprotein C-II precursor NP_000474.2:p.Glu60= NP_000474.2:p.Glu60Lys
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#.

54 SubSNP, 9 Frequency, 3 ClinVar submissions
No Submitter Submission ID Date (Build)
1 ARAVINDA ss6566 Sep 19, 2000 (52)
2 PERLEGEN ss69229173 May 17, 2007 (127)
3 AFFY ss74806867 Aug 16, 2007 (128)
4 ILLUMINA ss74877946 Dec 06, 2007 (129)
5 SEATTLESEQ ss159740189 Dec 01, 2009 (131)
6 ILLUMINA ss173909989 Jul 04, 2010 (132)
7 ILLUMINA ss244302814 Jul 04, 2010 (132)
8 OMIM-CURATED-RECORDS ss255603918 Aug 20, 2010 (132)
9 NHLBI-ESP ss342502272 May 09, 2011 (134)
10 ILLUMINA ss410938452 Sep 17, 2011 (135)
11 1000GENOMES ss465616696 Sep 17, 2011 (135)
12 1000GENOMES ss491161776 May 04, 2012 (137)
13 EXOME_CHIP ss491549572 May 04, 2012 (137)
14 ILLUMINA ss537305844 Sep 08, 2015 (146)
15 ILLUMINA ss780747111 Sep 08, 2015 (146)
16 ILLUMINA ss783424874 Sep 08, 2015 (146)
17 1000GENOMES ss1363327447 Aug 21, 2014 (142)
18 EVA_EXAC ss1693665900 Apr 01, 2015 (144)
19 ILLUMINA ss1752288254 Sep 08, 2015 (146)
20 ILLUMINA ss1917938939 Feb 12, 2016 (147)
21 WEILL_CORNELL_DGM ss1937836179 Feb 12, 2016 (147)
22 ILLUMINA ss1946537679 Feb 12, 2016 (147)
23 HUMAN_LONGEVITY ss2226014770 Dec 20, 2016 (150)
24 GNOMAD ss2744091401 Nov 08, 2017 (151)
25 GNOMAD ss2750219107 Nov 08, 2017 (151)
26 GNOMAD ss2963334155 Nov 08, 2017 (151)
27 AFFY ss2985144707 Nov 08, 2017 (151)
28 ILLUMINA ss3021911703 Nov 08, 2017 (151)
29 ILLUMINA ss3627941696 Oct 12, 2018 (152)
30 ILLUMINA ss3627941697 Oct 12, 2018 (152)
31 ILLUMINA ss3634738135 Oct 12, 2018 (152)
32 ILLUMINA ss3638229907 Oct 12, 2018 (152)
33 ILLUMINA ss3640445443 Oct 12, 2018 (152)
34 ILLUMINA ss3643202445 Oct 12, 2018 (152)
35 ILLUMINA ss3644726194 Oct 12, 2018 (152)
36 ILLUMINA ss3652337815 Oct 12, 2018 (152)
37 ILLUMINA ss3653917454 Oct 12, 2018 (152)
38 ILLUMINA ss3725733675 Jul 13, 2019 (153)
39 ILLUMINA ss3744466162 Jul 13, 2019 (153)
40 ILLUMINA ss3745038144 Jul 13, 2019 (153)
41 ILLUMINA ss3772535228 Jul 13, 2019 (153)
42 EVA ss3825301510 Apr 27, 2020 (154)
43 EVA ss3986802323 Apr 26, 2021 (155)
44 EVA ss4017826857 Apr 26, 2021 (155)
45 TOPMED ss5076176705 Apr 26, 2021 (155)
46 1000G_HIGH_COVERAGE ss5307396880 Oct 13, 2022 (156)
47 EVA ss5435089173 Oct 13, 2022 (156)
48 HUGCELL_USP ss5499892517 Oct 13, 2022 (156)
49 1000G_HIGH_COVERAGE ss5613192882 Oct 13, 2022 (156)
50 SANFORD_IMAGENETICS ss5662476231 Oct 13, 2022 (156)
51 EVA ss5847846277 Oct 13, 2022 (156)
52 EVA ss5928257436 Oct 13, 2022 (156)
53 EVA ss5953885951 Oct 13, 2022 (156)
54 EVA ss5979547924 Oct 13, 2022 (156)
55 1000Genomes NC_000019.9 - 45452080 Oct 12, 2018 (152)
56 1000Genomes_30x NC_000019.10 - 44948823 Oct 13, 2022 (156)
57 ExAC NC_000019.9 - 45452080 Oct 12, 2018 (152)
58 gnomAD - Genomes NC_000019.10 - 44948823 Apr 26, 2021 (155)
59 gnomAD - Exomes NC_000019.9 - 45452080 Jul 13, 2019 (153)
60 HapMap NC_000019.10 - 44948823 Apr 27, 2020 (154)
61 Qatari NC_000019.9 - 45452080 Apr 27, 2020 (154)
62 TopMed NC_000019.10 - 44948823 Apr 26, 2021 (155)
63 ALFA NC_000019.10 - 44948823 Apr 26, 2021 (155)
64 ClinVar RCV000002698.2 Oct 12, 2018 (152)
65 ClinVar RCV000991187.1 Apr 27, 2020 (154)
66 ClinVar RCV001513190.6 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)
rs52790555 Sep 21, 2007 (128)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss3643202445 NC_000019.8:50143919:G:A NC_000019.10:44948822:G:A (self)
76740029, 4174639, 13407147, 19878101, ss342502272, ss465616696, ss491161776, ss491549572, ss537305844, ss780747111, ss783424874, ss1363327447, ss1693665900, ss1752288254, ss1917938939, ss1937836179, ss1946537679, ss2744091401, ss2750219107, ss2963334155, ss2985144707, ss3021911703, ss3627941696, ss3627941697, ss3634738135, ss3638229907, ss3640445443, ss3644726194, ss3652337815, ss3653917454, ss3744466162, ss3745038144, ss3772535228, ss3825301510, ss3986802323, ss4017826857, ss5435089173, ss5662476231, ss5847846277, ss5953885951, ss5979547924 NC_000019.9:45452079:G:A NC_000019.10:44948822:G:A (self)
RCV000002698.2, RCV000991187.1, RCV001513190.6, 100718817, 541202942, 1701773, 291722369, 6173412943, ss255603918, ss2226014770, ss3725733675, ss5076176705, ss5307396880, ss5499892517, ss5613192882, ss5928257436 NC_000019.10:44948822:G:A NC_000019.10:44948822:G:A (self)
ss6566, ss69229173, ss74806867, ss74877946, ss159740189, ss173909989, ss244302814, ss410938452 NT_011109.16:17720297:G:A NC_000019.10:44948822:G:A (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 rs5122
PMID Title Author Year Journal
8490626 Molecular cloning and characteristics of a new apolipoprotein C-II mutant identified in three unrelated individuals with hypercholesterolemia and hypertriglyceridemia. Pullinger CR et al. 1993 Human molecular genetics
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