Name: rs17507066
Published: September 21, 2022
License: Open Access

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.

rs17507066

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr22:28696732 (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: C>T
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.056198 (14875/264690, TOPMED)
T=0.068780 (9640/140158, GnomAD)
T=0.09523 (3420/35912, ALFA) (+ 16 more)
T=0.00145 (41/28258, 14KJPN)
T=0.00161 (27/16760, 8.3KJPN)
T=0.0548 (351/6404, 1000G_30x)
T=0.0557 (279/5008, 1000G)
T=0.1908 (855/4480, Estonian)
T=0.0885 (341/3854, ALSPAC)
T=0.0801 (297/3708, TWINSUK)
T=0.0016 (3/1832, Korea1K)
T=0.088 (88/998, GoNL)
T=0.140 (84/600, NorthernSweden)
T=0.036 (12/330, HapMap)
T=0.019 (4/216, Qatari)
T=0.005 (1/216, Vietnamese)
C=0.46 (31/68, SGDP_PRJ)
T=0.05 (2/40, GENOME_DK)
C=0.35 (7/20, Siberian)

Clinical Significance: Reported in ClinVar
Gene : Consequence: CHEK2 : Intron 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: 20230706150541

Population	Group	Sample Size	Ref Allele	Alt Allele
Total	Global	35912	C=0.90477	T=0.09523
European	Sub	31016	C=0.89570	T=0.10430
African	Sub	2946	C=0.9830	T=0.0170
African Others	Sub	114	C=1.000	T=0.000
African American	Sub	2832	C=0.9823	T=0.0177
Asian	Sub	154	C=0.994	T=0.006
East Asian	Sub	128	C=0.992	T=0.008
Other Asian	Sub	26	C=1.00	T=0.00
Latin American 1	Sub	146	C=0.973	T=0.027
Latin American 2	Sub	610	C=0.916	T=0.084
South Asian	Sub	98	C=0.90	T=0.10
Other	Sub	942	C=0.927	T=0.073

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").

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Study	Population	Group	Sample Size	Ref Allele	Alt Allele
TopMed	Global	Study-wide	264690	C=0.943802	T=0.056198
gnomAD - Genomes	Global	Study-wide	140158	C=0.931220	T=0.068780
gnomAD - Genomes	European	Sub	75886	C=0.89623	T=0.10377
gnomAD - Genomes	African	Sub	42024	C=0.98306	T=0.01694
gnomAD - Genomes	American	Sub	13644	C=0.94071	T=0.05929
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	C=0.9693	T=0.0307
gnomAD - Genomes	East Asian	Sub	3132	C=0.9949	T=0.0051
gnomAD - Genomes	Other	Sub	2148	C=0.9413	T=0.0587
Allele Frequency Aggregator	Total	Global	35912	C=0.90477	T=0.09523
Allele Frequency Aggregator	European	Sub	31016	C=0.89570	T=0.10430
Allele Frequency Aggregator	African	Sub	2946	C=0.9830	T=0.0170
Allele Frequency Aggregator	Other	Sub	942	C=0.927	T=0.073
Allele Frequency Aggregator	Latin American 2	Sub	610	C=0.916	T=0.084
Allele Frequency Aggregator	Asian	Sub	154	C=0.994	T=0.006
Allele Frequency Aggregator	Latin American 1	Sub	146	C=0.973	T=0.027
Allele Frequency Aggregator	South Asian	Sub	98	C=0.90	T=0.10
14KJPN	JAPANESE	Study-wide	28258	C=0.99855	T=0.00145
8.3KJPN	JAPANESE	Study-wide	16760	C=0.99839	T=0.00161
1000Genomes_30x	Global	Study-wide	6404	C=0.9452	T=0.0548
1000Genomes_30x	African	Sub	1786	C=0.9950	T=0.0050
1000Genomes_30x	Europe	Sub	1266	C=0.9107	T=0.0893
1000Genomes_30x	South Asian	Sub	1202	C=0.8744	T=0.1256
1000Genomes_30x	East Asian	Sub	1170	C=0.9940	T=0.0060
1000Genomes_30x	American	Sub	980	C=0.928	T=0.072
1000Genomes	Global	Study-wide	5008	C=0.9443	T=0.0557
1000Genomes	African	Sub	1322	C=0.9947	T=0.0053
1000Genomes	East Asian	Sub	1008	C=0.9931	T=0.0069
1000Genomes	Europe	Sub	1006	C=0.9115	T=0.0885
1000Genomes	South Asian	Sub	978	C=0.872	T=0.128
1000Genomes	American	Sub	694	C=0.927	T=0.073
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.8092	T=0.1908
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.9115	T=0.0885
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.9199	T=0.0801
Korean Genome Project	KOREAN	Study-wide	1832	C=0.9984	T=0.0016
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.912	T=0.088
Northern Sweden	ACPOP	Study-wide	600	C=0.860	T=0.140
HapMap	Global	Study-wide	330	C=0.964	T=0.036
HapMap	African	Sub	120	C=1.000	T=0.000
HapMap	American	Sub	120	C=0.900	T=0.100
HapMap	Asian	Sub	90	C=1.00	T=0.00
Qatari	Global	Study-wide	216	C=0.981	T=0.019
A Vietnamese Genetic Variation Database	Global	Study-wide	216	C=0.995	T=0.005
SGDP_PRJ	Global	Study-wide	68	C=0.46	T=0.54
The Danish reference pan genome	Danish	Study-wide	40	C=0.95	T=0.05
Siberian	Global	Study-wide	20	C=0.35	T=0.65

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 22	NC_000022.11:g.28696732C>T
GRCh37.p13 chr 22	NC_000022.10:g.29092720C>T
CHEK2 RefSeqGene (LRG_302)	NG_008150.2:g.50135G>A

Gene: CHEK2, checkpoint kinase 2 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
CHEK2 transcript variant 3	NM_001005735.2:c.1224+169… NM_001005735.2:c.1224+169G>A	N/A	Intron Variant
CHEK2 transcript variant 4	NM_001257387.2:c.432+169G… NM_001257387.2:c.432+169G>A	N/A	Intron Variant
CHEK2 transcript variant 5	NM_001349956.2:c.894+169G… NM_001349956.2:c.894+169G>A	N/A	Intron Variant
CHEK2 transcript variant 1	NM_007194.4:c.1095+169G>A	N/A	Intron Variant
CHEK2 transcript variant 2	NM_145862.2:c.1009-859G>A	N/A	Intron Variant
CHEK2 transcript variant X12	XM_006724114.4:c.615+169G… XM_006724114.4:c.615+169G>A	N/A	Intron Variant
CHEK2 transcript variant X14	XM_006724116.3:c.552+169G… XM_006724116.3:c.552+169G>A	N/A	Intron Variant
CHEK2 transcript variant X1	XM_011529839.3:c.1254+169… XM_011529839.3:c.1254+169G>A	N/A	Intron Variant
CHEK2 transcript variant X4	XM_011529840.4:c.1168-859… XM_011529840.4:c.1168-859G>A	N/A	Intron Variant
CHEK2 transcript variant X10	XM_011529842.3:c.924+169G… XM_011529842.3:c.924+169G>A	N/A	Intron Variant
CHEK2 transcript variant X18	XM_011529845.3:c.432+169G… XM_011529845.3:c.432+169G>A	N/A	Intron Variant
CHEK2 transcript variant X2	XM_017028560.2:c.1218+169… XM_017028560.2:c.1218+169G>A	N/A	Intron Variant
CHEK2 transcript variant X6	XM_024452148.2:c.1125+169… XM_024452148.2:c.1125+169G>A	N/A	Intron Variant
CHEK2 transcript variant X9	XM_024452149.2:c.1039-859… XM_024452149.2:c.1039-859G>A	N/A	Intron Variant
CHEK2 transcript variant X3	XM_047441104.1:c.1188+169… XM_047441104.1:c.1188+169G>A	N/A	Intron Variant
CHEK2 transcript variant X5	XM_047441105.1:c.1138-859… XM_047441105.1:c.1138-859G>A	N/A	Intron Variant
CHEK2 transcript variant X7	XM_047441106.1:c.1102-859… XM_047441106.1:c.1102-859G>A	N/A	Intron Variant
CHEK2 transcript variant X8	XM_047441107.1:c.1053+169… XM_047441107.1:c.1053+169G>A	N/A	Intron Variant
CHEK2 transcript variant X13	XM_047441108.1:c.529-859G… XM_047441108.1:c.529-859G>A	N/A	Intron Variant
CHEK2 transcript variant X11	XM_011529844.3:c.	N/A	Genic Downstream Transcript Variant
CHEK2 transcript variant X16	XR_937806.3:n.	N/A	Intron Variant
CHEK2 transcript variant X15	XR_007067954.1:n.	N/A	Genic Downstream Transcript Variant
CHEK2 transcript variant X19	XR_007067955.1:n.	N/A	Genic Downstream Transcript Variant
CHEK2 transcript variant X17	XR_937807.3:n.	N/A	Genic Downstream Transcript Variant

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: T (allele ID: 1246879 )

ClinVar Accession	Disease Names	Clinical Significance
RCV001666533.2	not provided	Benign

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=	T
GRCh38.p14 chr 22	NC_000022.11:g.28696732=	NC_000022.11:g.28696732C>T
GRCh37.p13 chr 22	NC_000022.10:g.29092720=	NC_000022.10:g.29092720C>T
CHEK2 RefSeqGene (LRG_302)	NG_008150.2:g.50135=	NG_008150.2:g.50135G>A
CHEK2 transcript variant 3	NM_001005735.1:c.1224+169=	NM_001005735.1:c.1224+169G>A
CHEK2 transcript variant 3	NM_001005735.2:c.1224+169=	NM_001005735.2:c.1224+169G>A
CHEK2 transcript variant 4	NM_001257387.1:c.432+169=	NM_001257387.1:c.432+169G>A
CHEK2 transcript variant 4	NM_001257387.2:c.432+169=	NM_001257387.2:c.432+169G>A
CHEK2 transcript variant 5	NM_001349956.2:c.894+169=	NM_001349956.2:c.894+169G>A
CHEK2 transcript variant 1	NM_007194.3:c.1095+169=	NM_007194.3:c.1095+169G>A
CHEK2 transcript variant 1	NM_007194.4:c.1095+169=	NM_007194.4:c.1095+169G>A
CHEK2 transcript variant 2	NM_145862.2:c.1009-859=	NM_145862.2:c.1009-859G>A
CHEK2 transcript variant X12	XM_006724114.4:c.615+169=	XM_006724114.4:c.615+169G>A
CHEK2 transcript variant X14	XM_006724116.3:c.552+169=	XM_006724116.3:c.552+169G>A
CHEK2 transcript variant X1	XM_011529839.3:c.1254+169=	XM_011529839.3:c.1254+169G>A
CHEK2 transcript variant X4	XM_011529840.4:c.1168-859=	XM_011529840.4:c.1168-859G>A
CHEK2 transcript variant X10	XM_011529842.3:c.924+169=	XM_011529842.3:c.924+169G>A
CHEK2 transcript variant X18	XM_011529845.3:c.432+169=	XM_011529845.3:c.432+169G>A
CHEK2 transcript variant X2	XM_017028560.2:c.1218+169=	XM_017028560.2:c.1218+169G>A
CHEK2 transcript variant X6	XM_024452148.2:c.1125+169=	XM_024452148.2:c.1125+169G>A
CHEK2 transcript variant X9	XM_024452149.2:c.1039-859=	XM_024452149.2:c.1039-859G>A
CHEK2 transcript variant X3	XM_047441104.1:c.1188+169=	XM_047441104.1:c.1188+169G>A
CHEK2 transcript variant X5	XM_047441105.1:c.1138-859=	XM_047441105.1:c.1138-859G>A
CHEK2 transcript variant X7	XM_047441106.1:c.1102-859=	XM_047441106.1:c.1102-859G>A
CHEK2 transcript variant X8	XM_047441107.1:c.1053+169=	XM_047441107.1:c.1053+169G>A
CHEK2 transcript variant X13	XM_047441108.1:c.529-859=	XM_047441108.1:c.529-859G>A

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#.

44 SubSNP, 19 Frequency, 1 ClinVar submissions

No	Submitter	Submission ID	Date (Build)
1	PERLEGEN	ss24552164	Sep 20, 2004 (123)
2	EGP_SNPS	ss28531748	Dec 02, 2004 (126)
3	1000GENOMES	ss238047634	Jul 15, 2010 (132)
4	PJP	ss292749734	May 09, 2011 (134)
5	SSMP	ss662533363	Apr 25, 2013 (138)
6	EVA-GONL	ss995292432	Aug 21, 2014 (142)
7	JMKIDD_LAB	ss1082617056	Aug 21, 2014 (142)
8	1000GENOMES	ss1366947287	Aug 21, 2014 (142)
9	EVA_GENOME_DK	ss1579730047	Apr 01, 2015 (144)
10	EVA_UK10K_ALSPAC	ss1639878435	Apr 01, 2015 (144)
11	EVA_UK10K_TWINSUK	ss1682872468	Apr 01, 2015 (144)
12	EVA_DECODE	ss1699361486	Apr 01, 2015 (144)
13	WEILL_CORNELL_DGM	ss1938858705	Feb 12, 2016 (147)
14	JJLAB	ss2030201413	Sep 14, 2016 (149)
15	USC_VALOUEV	ss2158816678	Dec 20, 2016 (150)
16	HUMAN_LONGEVITY	ss2246887606	Dec 20, 2016 (150)
17	ILLUMINA	ss2635111549	Nov 08, 2017 (151)
18	ILLUMINA	ss2710955166	Nov 08, 2017 (151)
19	GNOMAD	ss2973762751	Nov 08, 2017 (151)
20	SWEGEN	ss3019212203	Nov 08, 2017 (151)
21	BIOINF_KMB_FNS_UNIBA	ss3028938278	Nov 08, 2017 (151)
22	CSHL	ss3352811315	Nov 08, 2017 (151)
23	EGCUT_WGS	ss3685709149	Jul 13, 2019 (153)
24	EVA_DECODE	ss3708086821	Jul 13, 2019 (153)
25	ACPOP	ss3743883653	Jul 13, 2019 (153)
26	EVA	ss3759314104	Jul 13, 2019 (153)
27	KHV_HUMAN_GENOMES	ss3822479404	Jul 13, 2019 (153)
28	EVA	ss3835962066	Apr 27, 2020 (154)
29	SGDP_PRJ	ss3890428759	Apr 27, 2020 (154)
30	KOGIC	ss3983526914	Apr 27, 2020 (154)
31	TOPMED	ss5107298237	Apr 27, 2021 (155)
32	TOMMO_GENOMICS	ss5232370663	Apr 27, 2021 (155)
33	1000G_HIGH_COVERAGE	ss5310906660	Oct 16, 2022 (156)
34	EVA	ss5440951939	Oct 16, 2022 (156)
35	HUGCELL_USP	ss5502766111	Oct 16, 2022 (156)
36	EVA	ss5512362489	Oct 16, 2022 (156)
37	1000G_HIGH_COVERAGE	ss5618374466	Oct 16, 2022 (156)
38	SANFORD_IMAGENETICS	ss5664386890	Oct 16, 2022 (156)
39	TOMMO_GENOMICS	ss5793409804	Oct 16, 2022 (156)
40	YY_MCH	ss5818663899	Oct 16, 2022 (156)
41	EVA	ss5821994970	Oct 16, 2022 (156)
42	EVA	ss5881602198	Oct 16, 2022 (156)
43	EVA	ss5959237786	Oct 16, 2022 (156)
44	EVA	ss5981321605	Oct 16, 2022 (156)
45	1000Genomes	NC_000022.10 - 29092720	Oct 12, 2018 (152)
46	1000Genomes_30x	NC_000022.11 - 28696732	Oct 16, 2022 (156)
47	The Avon Longitudinal Study of Parents and Children	NC_000022.10 - 29092720	Oct 12, 2018 (152)
48	Genetic variation in the Estonian population	NC_000022.10 - 29092720	Oct 12, 2018 (152)
49	The Danish reference pan genome	NC_000022.10 - 29092720	Apr 27, 2020 (154)
50	gnomAD - Genomes	NC_000022.11 - 28696732	Apr 27, 2021 (155)
51	Genome of the Netherlands Release 5	NC_000022.10 - 29092720	Apr 27, 2020 (154)
52	HapMap	NC_000022.11 - 28696732	Apr 27, 2020 (154)
53	Korean Genome Project	NC_000022.11 - 28696732	Apr 27, 2020 (154)
54	Northern Sweden	NC_000022.10 - 29092720	Jul 13, 2019 (153)
55	Qatari	NC_000022.10 - 29092720	Apr 27, 2020 (154)
56	SGDP_PRJ	NC_000022.10 - 29092720	Apr 27, 2020 (154)
57	Siberian	NC_000022.10 - 29092720	Apr 27, 2020 (154)
58	8.3KJPN	NC_000022.10 - 29092720	Apr 27, 2021 (155)
59	14KJPN	NC_000022.11 - 28696732	Oct 16, 2022 (156)
60	TopMed	NC_000022.11 - 28696732	Apr 27, 2021 (155)
61	UK 10K study - Twins	NC_000022.10 - 29092720	Oct 12, 2018 (152)
62	A Vietnamese Genetic Variation Database	NC_000022.10 - 29092720	Jul 13, 2019 (153)
63	ALFA	NC_000022.11 - 28696732	Apr 27, 2021 (155)
64	ClinVar	RCV001666533.2	Oct 16, 2022 (156)

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)
rs17883962	Mar 11, 2006 (126)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss292749734, ss1699361486, ss2635111549	NC_000022.9:27422719:C:T	NC_000022.11:28696731:C:T	(self)
80491096, 44520289, 31447397, 5894986, 19839251, 17168518, 20900627, 42445739, 11333032, 90339970, 44520289, 9823773, ss238047634, ss662533363, ss995292432, ss1082617056, ss1366947287, ss1579730047, ss1639878435, ss1682872468, ss1938858705, ss2030201413, ss2158816678, ss2710955166, ss2973762751, ss3019212203, ss3352811315, ss3685709149, ss3743883653, ss3759314104, ss3835962066, ss3890428759, ss5232370663, ss5440951939, ss5512362489, ss5664386890, ss5821994970, ss5959237786, ss5981321605	NC_000022.10:29092719:C:T	NC_000022.11:28696731:C:T	(self)
RCV001666533.2, 105900401, 568391634, 2242278, 39904915, 127246908, 382407184, 2283957443, ss2246887606, ss3028938278, ss3708086821, ss3822479404, ss3983526914, ss5107298237, ss5310906660, ss5502766111, ss5618374466, ss5793409804, ss5818663899, ss5881602198	NC_000022.11:28696731:C:T	NC_000022.11:28696731:C:T	(self)
ss24552164, ss28531748	NT_011520.12:8483288:C:T	NC_000022.11:28696731:C:T	(self)

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

1 citation for rs17507066

PMID	Title	Author	Year	Journal
27747004	Association of CHEK2 polymorphisms with the efficacy of platinum-based chemotherapy for advanced non-small-cell lung cancer in Chinese never-smoking women.	Xu W et al.	2016	Journal of thoracic disease

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.

Choose placement

dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs17507066