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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.

rs111498552

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr2:134921415 (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=0.201360 (53298/264690, TOPMED)
A=0.207633 (28996/139650, GnomAD)
A=0.13725 (3878/28256, 14KJPN) (+ 15 more)
A=0.22271 (4207/18890, ALFA)
A=0.13663 (2290/16760, 8.3KJPN)
A=0.1735 (1111/6404, 1000G_30x)
A=0.1749 (876/5008, 1000G)
A=0.2786 (1248/4480, Estonian)
A=0.1811 (698/3854, ALSPAC)
A=0.1920 (712/3708, TWINSUK)
A=0.0948 (277/2922, KOREAN)
A=0.0884 (162/1832, Korea1K)
A=0.186 (186/998, GoNL)
A=0.112 (67/600, NorthernSweden)
G=0.426 (92/216, Qatari)
G=0.365 (76/208, SGDP_PRJ)
A=0.17 (7/40, GENOME_DK)
G=0.42 (10/24, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
CCNT2 : Intron Variant
Publications
0 citations
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: 20230706150541
Population Group Sample Size Ref Allele Alt Allele
Total Global 18890 G=0.77729 A=0.22271
European Sub 14286 G=0.75738 A=0.24262
African Sub 2946 G=0.8568 A=0.1432
African Others Sub 114 G=0.842 A=0.158
African American Sub 2832 G=0.8573 A=0.1427
Asian Sub 112 G=0.946 A=0.054
East Asian Sub 86 G=0.95 A=0.05
Other Asian Sub 26 G=0.92 A=0.08
Latin American 1 Sub 146 G=0.733 A=0.267
Latin American 2 Sub 610 G=0.811 A=0.189
South Asian Sub 98 G=0.81 A=0.19
Other Sub 692 G=0.798 A=0.202


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=0.798640 A=0.201360
gnomAD - Genomes Global Study-wide 139650 G=0.792367 A=0.207633
gnomAD - Genomes European Sub 75668 G=0.77323 A=0.22677
gnomAD - Genomes African Sub 41790 G=0.84884 A=0.15116
gnomAD - Genomes American Sub 13608 G=0.74206 A=0.25794
gnomAD - Genomes Ashkenazi Jewish Sub 3324 G=0.5743 A=0.4257
gnomAD - Genomes East Asian Sub 3122 G=0.9641 A=0.0359
gnomAD - Genomes Other Sub 2138 G=0.7741 A=0.2259
14KJPN JAPANESE Study-wide 28256 G=0.86275 A=0.13725
Allele Frequency Aggregator Total Global 18890 G=0.77729 A=0.22271
Allele Frequency Aggregator European Sub 14286 G=0.75738 A=0.24262
Allele Frequency Aggregator African Sub 2946 G=0.8568 A=0.1432
Allele Frequency Aggregator Other Sub 692 G=0.798 A=0.202
Allele Frequency Aggregator Latin American 2 Sub 610 G=0.811 A=0.189
Allele Frequency Aggregator Latin American 1 Sub 146 G=0.733 A=0.267
Allele Frequency Aggregator Asian Sub 112 G=0.946 A=0.054
Allele Frequency Aggregator South Asian Sub 98 G=0.81 A=0.19
8.3KJPN JAPANESE Study-wide 16760 G=0.86337 A=0.13663
1000Genomes_30x Global Study-wide 6404 G=0.8265 A=0.1735
1000Genomes_30x African Sub 1786 G=0.8494 A=0.1506
1000Genomes_30x Europe Sub 1266 G=0.7306 A=0.2694
1000Genomes_30x South Asian Sub 1202 G=0.7937 A=0.2063
1000Genomes_30x East Asian Sub 1170 G=0.9453 A=0.0547
1000Genomes_30x American Sub 980 G=0.807 A=0.193
1000Genomes Global Study-wide 5008 G=0.8251 A=0.1749
1000Genomes African Sub 1322 G=0.8442 A=0.1558
1000Genomes East Asian Sub 1008 G=0.9454 A=0.0546
1000Genomes Europe Sub 1006 G=0.7207 A=0.2793
1000Genomes South Asian Sub 978 G=0.801 A=0.199
1000Genomes American Sub 694 G=0.800 A=0.200
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.7214 A=0.2786
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.8189 A=0.1811
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.8080 A=0.1920
KOREAN population from KRGDB KOREAN Study-wide 2922 G=0.9052 A=0.0948
Korean Genome Project KOREAN Study-wide 1832 G=0.9116 A=0.0884
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.814 A=0.186
Northern Sweden ACPOP Study-wide 600 G=0.888 A=0.112
Qatari Global Study-wide 216 G=0.426 A=0.574
SGDP_PRJ Global Study-wide 208 G=0.365 A=0.635
The Danish reference pan genome Danish Study-wide 40 G=0.82 A=0.17
Siberian Global Study-wide 24 G=0.42 A=0.58
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 2 NC_000002.12:g.134921415G>A
GRCh37.p13 chr 2 NC_000002.11:g.135678985G>A
CCNT2 RefSeqGene NG_029189.1:g.7594G>A
Gene: CCNT2, cyclin T2 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
CCNT2 transcript variant a NM_001241.4:c.240+1524G>A N/A Intron Variant
CCNT2 transcript variant d NM_001320748.2:c.-287+152…

NM_001320748.2:c.-287+1524G>A

 		N/A Intron Variant
CCNT2 transcript variant e NM_001320749.2:c.-373+152…

NM_001320749.2:c.-373+1524G>A

 		N/A Intron Variant
CCNT2 transcript variant b NM_058241.3:c.240+1524G>A N/A Intron Variant
CCNT2 transcript variant c NR_037649.2:n. N/A Intron Variant
CCNT2 transcript variant f NR_135468.2:n. N/A Intron Variant
CCNT2 transcript variant X1 XM_017005227.2:c.240+1524…

XM_017005227.2:c.240+1524G>A

 		N/A Intron Variant
CCNT2 transcript variant X2 XM_017005228.3:c.240+1524…

XM_017005228.3:c.240+1524G>A

 		N/A Intron Variant
CCNT2 transcript variant X3 XM_047446259.1:c. N/A Genic Upstream Transcript Variant
CCNT2 transcript variant X4 XM_047446260.1:c. N/A Genic Upstream 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.

Not Reported in ClinVar
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 2 NC_000002.12:g.134921415= NC_000002.12:g.134921415G>A
GRCh37.p13 chr 2 NC_000002.11:g.135678985= NC_000002.11:g.135678985G>A
CCNT2 RefSeqGene NG_029189.1:g.7594= NG_029189.1:g.7594G>A
CCNT2 transcript variant a NM_001241.3:c.240+1524= NM_001241.3:c.240+1524G>A
CCNT2 transcript variant a NM_001241.4:c.240+1524= NM_001241.4:c.240+1524G>A
CCNT2 transcript variant d NM_001320748.2:c.-287+1524= NM_001320748.2:c.-287+1524G>A
CCNT2 transcript variant e NM_001320749.2:c.-373+1524= NM_001320749.2:c.-373+1524G>A
CCNT2 transcript variant b NM_058241.2:c.240+1524= NM_058241.2:c.240+1524G>A
CCNT2 transcript variant b NM_058241.3:c.240+1524= NM_058241.3:c.240+1524G>A
CCNT2 transcript variant X1 XM_005263830.1:c.240+1524= XM_005263830.1:c.240+1524G>A
CCNT2 transcript variant X4 XM_005263833.1:c.-373+1524= XM_005263833.1:c.-373+1524G>A
CCNT2 transcript variant X1 XM_017005227.2:c.240+1524= XM_017005227.2:c.240+1524G>A
CCNT2 transcript variant X2 XM_017005228.3:c.240+1524= XM_017005228.3:c.240+1524G>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#.

48 SubSNP, 18 Frequency submissions
No Submitter Submission ID Date (Build)
1 COMPLETE_GENOMICS ss165273335 Jul 04, 2010 (132)
2 COMPLETE_GENOMICS ss167205267 Jul 04, 2010 (132)
3 1000GENOMES ss219526056 Jul 14, 2010 (132)
4 1000GENOMES ss231372630 Jul 14, 2010 (132)
5 GMI ss276691868 May 04, 2012 (137)
6 TISHKOFF ss555893809 Apr 25, 2013 (138)
7 SSMP ss649521200 Apr 25, 2013 (138)
8 EVA-GONL ss977386216 Aug 21, 2014 (142)
9 JMKIDD_LAB ss1069516527 Aug 21, 2014 (142)
10 1000GENOMES ss1299437174 Aug 21, 2014 (142)
11 DDI ss1428749058 Apr 01, 2015 (144)
12 EVA_GENOME_DK ss1579097703 Apr 01, 2015 (144)
13 EVA_DECODE ss1586814586 Apr 01, 2015 (144)
14 EVA_UK10K_ALSPAC ss1604621815 Apr 01, 2015 (144)
15 EVA_UK10K_TWINSUK ss1647615848 Apr 01, 2015 (144)
16 HAMMER_LAB ss1797573282 Sep 08, 2015 (146)
17 WEILL_CORNELL_DGM ss1920644654 Feb 12, 2016 (147)
18 JJLAB ss2020846246 Sep 14, 2016 (149)
19 USC_VALOUEV ss2148912277 Dec 20, 2016 (150)
20 HUMAN_LONGEVITY ss2234498843 Dec 20, 2016 (150)
21 GRF ss2703536715 Nov 08, 2017 (151)
22 GNOMAD ss2779972602 Nov 08, 2017 (151)
23 SWEGEN ss2990473360 Nov 08, 2017 (151)
24 BIOINF_KMB_FNS_UNIBA ss3024186527 Nov 08, 2017 (151)
25 CSHL ss3344494073 Nov 08, 2017 (151)
26 EGCUT_WGS ss3658315459 Jul 13, 2019 (153)
27 EVA_DECODE ss3704945121 Jul 13, 2019 (153)
28 ACPOP ss3728891023 Jul 13, 2019 (153)
29 EVA ss3757415374 Jul 13, 2019 (153)
30 KHV_HUMAN_GENOMES ss3801782788 Jul 13, 2019 (153)
31 EVA ss3827234605 Apr 25, 2020 (154)
32 SGDP_PRJ ss3853472285 Apr 25, 2020 (154)
33 KRGDB ss3899032581 Apr 25, 2020 (154)
34 KOGIC ss3949023076 Apr 25, 2020 (154)
35 TOPMED ss4524874425 Apr 26, 2021 (155)
36 TOMMO_GENOMICS ss5153990755 Apr 26, 2021 (155)
37 1000G_HIGH_COVERAGE ss5250111360 Oct 12, 2022 (156)
38 EVA ss5332515309 Oct 12, 2022 (156)
39 HUGCELL_USP ss5449914408 Oct 12, 2022 (156)
40 EVA ss5506598207 Oct 12, 2022 (156)
41 1000G_HIGH_COVERAGE ss5526429067 Oct 12, 2022 (156)
42 SANFORD_IMAGENETICS ss5629863611 Oct 12, 2022 (156)
43 TOMMO_GENOMICS ss5684153173 Oct 12, 2022 (156)
44 YY_MCH ss5802747756 Oct 12, 2022 (156)
45 EVA ss5820843338 Oct 12, 2022 (156)
46 EVA ss5852725555 Oct 12, 2022 (156)
47 EVA ss5932480732 Oct 12, 2022 (156)
48 EVA ss5956065595 Oct 12, 2022 (156)
49 1000Genomes NC_000002.11 - 135678985 Oct 11, 2018 (152)
50 1000Genomes_30x NC_000002.12 - 134921415 Oct 12, 2022 (156)
51 The Avon Longitudinal Study of Parents and Children NC_000002.11 - 135678985 Oct 11, 2018 (152)
52 Genetic variation in the Estonian population NC_000002.11 - 135678985 Oct 11, 2018 (152)
53 The Danish reference pan genome NC_000002.11 - 135678985 Apr 25, 2020 (154)
54 gnomAD - Genomes NC_000002.12 - 134921415 Apr 26, 2021 (155)
55 Genome of the Netherlands Release 5 NC_000002.11 - 135678985 Apr 25, 2020 (154)
56 KOREAN population from KRGDB NC_000002.11 - 135678985 Apr 25, 2020 (154)
57 Korean Genome Project NC_000002.12 - 134921415 Apr 25, 2020 (154)
58 Northern Sweden NC_000002.11 - 135678985 Jul 13, 2019 (153)
59 Qatari NC_000002.11 - 135678985 Apr 25, 2020 (154)
60 SGDP_PRJ NC_000002.11 - 135678985 Apr 25, 2020 (154)
61 Siberian NC_000002.11 - 135678985 Apr 25, 2020 (154)
62 8.3KJPN NC_000002.11 - 135678985 Apr 26, 2021 (155)
63 14KJPN NC_000002.12 - 134921415 Oct 12, 2022 (156)
64 TopMed NC_000002.12 - 134921415 Apr 26, 2021 (155)
65 UK 10K study - Twins NC_000002.11 - 135678985 Oct 11, 2018 (152)
66 ALFA NC_000002.12 - 134921415 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).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss165273335, ss167205267, ss276691868, ss1586814586 NC_000002.10:135395454:G:A NC_000002.12:134921414:G:A (self)
10456888, 5759504, 4053707, 5262642, 2532217, 6209975, 2175888, 2686584, 5489265, 1428631, 11960062, 5759504, ss219526056, ss231372630, ss555893809, ss649521200, ss977386216, ss1069516527, ss1299437174, ss1428749058, ss1579097703, ss1604621815, ss1647615848, ss1797573282, ss1920644654, ss2020846246, ss2148912277, ss2703536715, ss2779972602, ss2990473360, ss3344494073, ss3658315459, ss3728891023, ss3757415374, ss3827234605, ss3853472285, ss3899032581, ss5153990755, ss5332515309, ss5506598207, ss5629863611, ss5820843338, ss5956065595 NC_000002.11:135678984:G:A NC_000002.12:134921414:G:A (self)
13955002, 74549356, 5401077, 17990277, 328697304, 11313738086, ss2234498843, ss3024186527, ss3704945121, ss3801782788, ss3949023076, ss4524874425, ss5250111360, ss5449914408, ss5526429067, ss5684153173, ss5802747756, ss5852725555, ss5932480732 NC_000002.12:134921414:G:A NC_000002.12:134921414: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.

No publications for rs111498552

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.post761+d5e8e07