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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.

rs2699895

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr3:179203851 (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
C>A
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.410767 (108726/264690, TOPMED)
C=0.416214 (58260/139976, GnomAD)
C=0.45066 (8513/18890, ALFA) (+ 14 more)
A=0.19821 (3322/16760, 8.3KJPN)
C=0.4820 (2414/5008, 1000G)
A=0.4460 (1998/4480, Estonian)
C=0.4741 (1827/3854, ALSPAC)
C=0.4703 (1744/3708, TWINSUK)
A=0.1884 (552/2930, KOREAN)
A=0.489 (488/998, GoNL)
A=0.445 (267/600, NorthernSweden)
A=0.292 (156/534, MGP)
C=0.290 (108/372, SGDP_PRJ)
C=0.259 (56/216, Qatari)
A=0.204 (44/216, Vietnamese)
C=0.45 (18/40, GENOME_DK)
C=0.32 (11/34, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
PIK3CA : Intron 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 3 NC_000003.12:g.179203851C>A
GRCh37.p13 chr 3 NC_000003.11:g.178921639C>A
PIK3CA RefSeqGene (LRG_310) NG_012113.2:g.60329C>A
Gene: PIK3CA, phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha (plus strand)
Molecule type Change Amino acid[Codon] SO Term
PIK3CA transcript NM_006218.4:c.1059+62C>A N/A Intron Variant
PIK3CA transcript variant X2 XM_006713658.4:c.1059+62C…

XM_006713658.4:c.1059+62C>A

N/A Intron Variant
PIK3CA transcript variant X1 XM_011512894.2:c.1059+62C…

XM_011512894.2:c.1059+62C>A

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 (New)
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 C=0.45066 A=0.54934
European Sub 14286 C=0.48985 A=0.51015
African Sub 2946 C=0.2553 A=0.7447
African Others Sub 114 C=0.202 A=0.798
African American Sub 2832 C=0.2574 A=0.7426
Asian Sub 112 C=0.777 A=0.223
East Asian Sub 86 C=0.78 A=0.22
Other Asian Sub 26 C=0.77 A=0.23
Latin American 1 Sub 146 C=0.336 A=0.664
Latin American 2 Sub 610 C=0.485 A=0.515
South Asian Sub 98 C=0.48 A=0.52
Other Sub 692 C=0.410 A=0.590


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 C=0.410767 A=0.589233
gnomAD - Genomes Global Study-wide 139976 C=0.416214 A=0.583786
gnomAD - Genomes European Sub 75776 C=0.48393 A=0.51607
gnomAD - Genomes African Sub 41966 C=0.24077 A=0.75923
gnomAD - Genomes American Sub 13640 C=0.49377 A=0.50623
gnomAD - Genomes Ashkenazi Jewish Sub 3324 C=0.4260 A=0.5740
gnomAD - Genomes East Asian Sub 3124 C=0.7702 A=0.2298
gnomAD - Genomes Other Sub 2146 C=0.4329 A=0.5671
8.3KJPN JAPANESE Study-wide 16760 C=0.80179 A=0.19821
1000Genomes Global Study-wide 5008 C=0.4820 A=0.5180
1000Genomes African Sub 1322 C=0.2133 A=0.7867
1000Genomes East Asian Sub 1008 C=0.7917 A=0.2083
1000Genomes Europe Sub 1006 C=0.4821 A=0.5179
1000Genomes South Asian Sub 978 C=0.531 A=0.469
1000Genomes American Sub 694 C=0.476 A=0.524
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.5540 A=0.4460
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.4741 A=0.5259
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.4703 A=0.5297
KOREAN population from KRGDB KOREAN Study-wide 2930 C=0.8116 A=0.1884
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 C=0.511 A=0.489
Northern Sweden ACPOP Study-wide 600 C=0.555 A=0.445
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 C=0.708 A=0.292
SGDP_PRJ Global Study-wide 372 C=0.290 A=0.710
Qatari Global Study-wide 216 C=0.259 A=0.741
A Vietnamese Genetic Variation Database Global Study-wide 216 C=0.796 A=0.204
The Danish reference pan genome Danish Study-wide 40 C=0.45 A=0.55
Siberian Global Study-wide 34 C=0.32 A=0.68
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 C= A
GRCh38.p13 chr 3 NC_000003.12:g.179203851= NC_000003.12:g.179203851C>A
GRCh37.p13 chr 3 NC_000003.11:g.178921639= NC_000003.11:g.178921639C>A
PIK3CA RefSeqGene (LRG_310) NG_012113.2:g.60329= NG_012113.2:g.60329C>A
PIK3CA transcript NM_006218.2:c.1059+62= NM_006218.2:c.1059+62C>A
PIK3CA transcript NM_006218.4:c.1059+62= NM_006218.4:c.1059+62C>A
PIK3CA transcript variant X2 XM_006713658.4:c.1059+62= XM_006713658.4:c.1059+62C>A
PIK3CA transcript variant X1 XM_011512894.2:c.1059+62= XM_011512894.2:c.1059+62C>A
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#.

69 SubSNP, 17 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_JCM ss3815240 Sep 28, 2001 (100)
2 WIPGA ss4915600 Aug 28, 2002 (108)
3 WI_SSAHASNP ss11559035 Jul 11, 2003 (116)
4 BCM_SSAHASNP ss14189788 Dec 05, 2003 (119)
5 CSHL-HAPMAP ss17739846 Feb 27, 2004 (120)
6 SSAHASNP ss21975960 Apr 05, 2004 (121)
7 IMCJ-GDT ss28503385 Sep 24, 2004 (126)
8 ABI ss44383224 Mar 10, 2006 (126)
9 HGSV ss85558967 Dec 15, 2007 (130)
10 BCMHGSC_JDW ss92388644 Mar 23, 2008 (129)
11 HUMANGENOME_JCVI ss99153360 Feb 05, 2009 (130)
12 SNP500CANCER ss105436879 Feb 05, 2009 (130)
13 1000GENOMES ss111434414 Jan 25, 2009 (130)
14 1000GENOMES ss112732838 Jan 25, 2009 (130)
15 ILLUMINA-UK ss117399111 Feb 14, 2009 (130)
16 ENSEMBL ss135414005 Dec 01, 2009 (131)
17 ENSEMBL ss139318729 Dec 01, 2009 (131)
18 COMPLETE_GENOMICS ss165116327 Jul 04, 2010 (132)
19 BUSHMAN ss203590655 Jul 04, 2010 (132)
20 BCM-HGSC-SUB ss206049503 Jul 04, 2010 (132)
21 1000GENOMES ss220610220 Jul 14, 2010 (132)
22 1000GENOMES ss232164984 Jul 14, 2010 (132)
23 1000GENOMES ss239506668 Jul 15, 2010 (132)
24 GMI ss277476912 May 04, 2012 (137)
25 GMI ss284803430 Apr 25, 2013 (138)
26 PJP ss292984314 May 09, 2011 (134)
27 TISHKOFF ss557151743 Apr 25, 2013 (138)
28 SSMP ss650897455 Apr 25, 2013 (138)
29 EVA-GONL ss979512710 Aug 21, 2014 (142)
30 JMKIDD_LAB ss1071098209 Aug 21, 2014 (142)
31 1000GENOMES ss1307484588 Aug 21, 2014 (142)
32 DDI ss1429689912 Apr 01, 2015 (144)
33 EVA_GENOME_DK ss1580318726 Apr 01, 2015 (144)
34 EVA_DECODE ss1589008966 Apr 01, 2015 (144)
35 EVA_UK10K_ALSPAC ss1608917574 Apr 01, 2015 (144)
36 EVA_UK10K_TWINSUK ss1651911607 Apr 01, 2015 (144)
37 EVA_MGP ss1711041879 Apr 01, 2015 (144)
38 HAMMER_LAB ss1800522623 Sep 08, 2015 (146)
39 WEILL_CORNELL_DGM ss1922733713 Feb 12, 2016 (147)
40 GENOMED ss1966658477 Feb 12, 2016 (147)
41 JJLAB ss2021942930 Sep 14, 2016 (149)
42 USC_VALOUEV ss2150040475 Dec 20, 2016 (150)
43 HUMAN_LONGEVITY ss2258607715 Dec 20, 2016 (150)
44 TOPMED ss2426007548 Dec 20, 2016 (150)
45 SYSTEMSBIOZJU ss2625470630 Nov 08, 2017 (151)
46 GRF ss2705463004 Nov 08, 2017 (151)
47 GNOMAD ss2802939201 Nov 08, 2017 (151)
48 SWEGEN ss2993727763 Nov 08, 2017 (151)
49 BIOINF_KMB_FNS_UNIBA ss3024740110 Nov 08, 2017 (151)
50 CSHL ss3345419911 Nov 08, 2017 (151)
51 TOPMED ss3414267113 Nov 08, 2017 (151)
52 URBANLAB ss3647597910 Oct 12, 2018 (152)
53 EGCUT_WGS ss3661683679 Jul 13, 2019 (153)
54 EVA_DECODE ss3710930384 Jul 13, 2019 (153)
55 ACPOP ss3730640615 Jul 13, 2019 (153)
56 EVA ss3761099394 Jul 13, 2019 (153)
57 KHV_HUMAN_GENOMES ss3804236451 Jul 13, 2019 (153)
58 EVA ss3828245521 Apr 25, 2020 (154)
59 EVA ss3837555001 Apr 25, 2020 (154)
60 EVA ss3842987366 Apr 25, 2020 (154)
61 SGDP_PRJ ss3857672909 Apr 25, 2020 (154)
62 KRGDB ss3903751541 Apr 25, 2020 (154)
63 FSA-LAB ss3984268454 Apr 26, 2021 (155)
64 FSA-LAB ss3984268455 Apr 26, 2021 (155)
65 EVA ss3986262258 Apr 26, 2021 (155)
66 TOPMED ss4595224085 Apr 26, 2021 (155)
67 TOMMO_GENOMICS ss5163082217 Apr 26, 2021 (155)
68 CPQ_GEN_INCA ss5236854751 Apr 26, 2021 (155)
69 CPQ_GEN_INCA ss5236859803 Apr 26, 2021 (155)
70 1000Genomes NC_000003.11 - 178921639 Oct 12, 2018 (152)
71 The Avon Longitudinal Study of Parents and Children NC_000003.11 - 178921639 Oct 12, 2018 (152)
72 Genetic variation in the Estonian population NC_000003.11 - 178921639 Oct 12, 2018 (152)
73 The Danish reference pan genome NC_000003.11 - 178921639 Apr 25, 2020 (154)
74 gnomAD - Genomes NC_000003.12 - 179203851 Apr 26, 2021 (155)
75 Genome of the Netherlands Release 5 NC_000003.11 - 178921639 Apr 25, 2020 (154)
76 KOREAN population from KRGDB NC_000003.11 - 178921639 Apr 25, 2020 (154)
77 Medical Genome Project healthy controls from Spanish population NC_000003.11 - 178921639 Apr 25, 2020 (154)
78 Northern Sweden NC_000003.11 - 178921639 Jul 13, 2019 (153)
79 Qatari NC_000003.11 - 178921639 Apr 25, 2020 (154)
80 SGDP_PRJ NC_000003.11 - 178921639 Apr 25, 2020 (154)
81 Siberian NC_000003.11 - 178921639 Apr 25, 2020 (154)
82 8.3KJPN NC_000003.11 - 178921639 Apr 26, 2021 (155)
83 TopMed NC_000003.12 - 179203851 Apr 26, 2021 (155)
84 UK 10K study - Twins NC_000003.11 - 178921639 Oct 12, 2018 (152)
85 A Vietnamese Genetic Variation Database NC_000003.11 - 178921639 Jul 13, 2019 (153)
86 ALFA NC_000003.12 - 179203851 Apr 26, 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).

Associated ID History Updated (Build)
rs3729675 Oct 09, 2002 (108)
rs17849083 Mar 10, 2006 (126)
rs58572914 May 24, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss85558967 NC_000003.9:180404340:C:A NC_000003.12:179203850:C:A (self)
ss92388644, ss111434414, ss112732838, ss117399111, ss165116327, ss203590655, ss206049503, ss277476912, ss284803430, ss292984314, ss1589008966 NC_000003.10:180404332:C:A NC_000003.12:179203850:C:A (self)
18799334, 10476497, 7421927, 6483665, 4605653, 10928935, 157639, 3925480, 4775643, 9689889, 2556829, 21051524, 10476497, 2292405, ss220610220, ss232164984, ss239506668, ss557151743, ss650897455, ss979512710, ss1071098209, ss1307484588, ss1429689912, ss1580318726, ss1608917574, ss1651911607, ss1711041879, ss1800522623, ss1922733713, ss1966658477, ss2021942930, ss2150040475, ss2426007548, ss2625470630, ss2705463004, ss2802939201, ss2993727763, ss3345419911, ss3661683679, ss3730640615, ss3761099394, ss3828245521, ss3837555001, ss3857672909, ss3903751541, ss3984268454, ss3984268455, ss3986262258, ss5163082217, ss5236854751, ss5236859803 NC_000003.11:178921638:C:A NC_000003.12:179203850:C:A (self)
133534793, 270411057, 432601640, 5655546071, ss2258607715, ss3024740110, ss3414267113, ss3647597910, ss3710930384, ss3804236451, ss3842987366, ss4595224085 NC_000003.12:179203850:C:A NC_000003.12:179203850:C:A (self)
ss14189788, ss17739846, ss21975960 NT_005612.14:85416796:C:A NC_000003.12:179203850:C:A (self)
ss3815240, ss4915600, ss28503385, ss44383224, ss99153360, ss105436879, ss135414005, ss139318729 NT_005612.16:85416784:C:A NC_000003.12:179203850:C:A (self)
ss11559035 NT_005962.15:14134101:C:A NC_000003.12:179203850:C:A (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 rs2699895

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