Name: rs207936
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.

rs207936

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr2:216175310 (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=0.223881 (59259/264690, TOPMED)
T=0.241244 (33793/140078, GnomAD)
T=0.30345 (10761/35462, ALFA) (+ 17 more)
T=0.06261 (1769/28256, 14KJPN)
T=0.06378 (1069/16760, 8.3KJPN)
T=0.1516 (971/6404, 1000G_30x)
T=0.1524 (763/5008, 1000G)
T=0.3379 (1514/4480, Estonian)
T=0.3625 (1397/3854, ALSPAC)
T=0.3670 (1361/3708, TWINSUK)
T=0.0421 (123/2922, KOREAN)
T=0.1224 (231/1888, HapMap)
T=0.347 (346/998, GoNL)
T=0.288 (173/600, NorthernSweden)
T=0.287 (153/534, MGP)
T=0.227 (49/216, Qatari)
T=0.053 (11/208, Vietnamese)
C=0.456 (83/182, SGDP_PRJ)
T=0.28 (11/40, GENOME_DK)
C=0.41 (9/22, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: XRCC5 : 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	35462	C=0.69655	T=0.30345
European	Sub	28940	C=0.65701	T=0.34299
African	Sub	4286	C=0.9174	T=0.0826
African Others	Sub	158	C=0.949	T=0.051
African American	Sub	4128	C=0.9162	T=0.0838
Asian	Sub	132	C=0.932	T=0.068
East Asian	Sub	106	C=0.934	T=0.066
Other Asian	Sub	26	C=0.92	T=0.08
Latin American 1	Sub	174	C=0.787	T=0.213
Latin American 2	Sub	748	C=0.830	T=0.170
South Asian	Sub	114	C=0.772	T=0.228
Other	Sub	1068	C=0.7360	T=0.2640

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=0.776119	T=0.223881
gnomAD - Genomes	Global	Study-wide	140078	C=0.758756	T=0.241244
gnomAD - Genomes	European	Sub	75830	C=0.66248	T=0.33752
gnomAD - Genomes	African	Sub	42004	C=0.91137	T=0.08863
gnomAD - Genomes	American	Sub	13642	C=0.79138	T=0.20862
gnomAD - Genomes	Ashkenazi Jewish	Sub	3322	C=0.6999	T=0.3001
gnomAD - Genomes	East Asian	Sub	3132	C=0.9521	T=0.0479
gnomAD - Genomes	Other	Sub	2148	C=0.7751	T=0.2249
Allele Frequency Aggregator	Total	Global	35462	C=0.69655	T=0.30345
Allele Frequency Aggregator	European	Sub	28940	C=0.65701	T=0.34299
Allele Frequency Aggregator	African	Sub	4286	C=0.9174	T=0.0826
Allele Frequency Aggregator	Other	Sub	1068	C=0.7360	T=0.2640
Allele Frequency Aggregator	Latin American 2	Sub	748	C=0.830	T=0.170
Allele Frequency Aggregator	Latin American 1	Sub	174	C=0.787	T=0.213
Allele Frequency Aggregator	Asian	Sub	132	C=0.932	T=0.068
Allele Frequency Aggregator	South Asian	Sub	114	C=0.772	T=0.228
14KJPN	JAPANESE	Study-wide	28256	C=0.93739	T=0.06261
8.3KJPN	JAPANESE	Study-wide	16760	C=0.93622	T=0.06378
1000Genomes_30x	Global	Study-wide	6404	C=0.8484	T=0.1516
1000Genomes_30x	African	Sub	1786	C=0.9591	T=0.0409
1000Genomes_30x	Europe	Sub	1266	C=0.6872	T=0.3128
1000Genomes_30x	South Asian	Sub	1202	C=0.8103	T=0.1897
1000Genomes_30x	East Asian	Sub	1170	C=0.9368	T=0.0632
1000Genomes_30x	American	Sub	980	C=0.796	T=0.204
1000Genomes	Global	Study-wide	5008	C=0.8476	T=0.1524
1000Genomes	African	Sub	1322	C=0.9554	T=0.0446
1000Genomes	East Asian	Sub	1008	C=0.9415	T=0.0585
1000Genomes	Europe	Sub	1006	C=0.6918	T=0.3082
1000Genomes	South Asian	Sub	978	C=0.801	T=0.199
1000Genomes	American	Sub	694	C=0.798	T=0.202
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.6621	T=0.3379
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.6375	T=0.3625
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.6330	T=0.3670
KOREAN population from KRGDB	KOREAN	Study-wide	2922	C=0.9579	T=0.0421
HapMap	Global	Study-wide	1888	C=0.8776	T=0.1224
HapMap	American	Sub	770	C=0.806	T=0.194
HapMap	African	Sub	688	C=0.978	T=0.022
HapMap	Asian	Sub	254	C=0.949	T=0.051
HapMap	Europe	Sub	176	C=0.693	T=0.307
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.653	T=0.347
Northern Sweden	ACPOP	Study-wide	600	C=0.712	T=0.288
Medical Genome Project healthy controls from Spanish population	Spanish controls	Study-wide	534	C=0.713	T=0.287
Qatari	Global	Study-wide	216	C=0.773	T=0.227
A Vietnamese Genetic Variation Database	Global	Study-wide	208	C=0.947	T=0.053
SGDP_PRJ	Global	Study-wide	182	C=0.456	T=0.544
The Danish reference pan genome	Danish	Study-wide	40	C=0.72	T=0.28
Siberian	Global	Study-wide	22	C=0.41	T=0.59

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.216175310C>T
GRCh37.p13 chr 2	NC_000002.11:g.217040033C>T
XRCC5 RefSeqGene	NG_029780.1:g.71014C>T
LOC100421349 pseudogene	NG_023660.1:g.729G>A

Gene: XRCC5, X-ray repair cross complementing 5 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
XRCC5 transcript	NM_021141.4:c.1834+13262C… NM_021141.4:c.1834+13262C>T	N/A	Intron 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.

Not Reported in ClinVar

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 2	NC_000002.12:g.216175310=	NC_000002.12:g.216175310C>T
GRCh37.p13 chr 2	NC_000002.11:g.217040033=	NC_000002.11:g.217040033C>T
XRCC5 RefSeqGene	NG_029780.1:g.71014=	NG_029780.1:g.71014C>T
LOC100421349 pseudogene	NG_023660.1:g.729=	NG_023660.1:g.729G>A
XRCC5 transcript	NM_021141.3:c.1834+13262=	NM_021141.3:c.1834+13262C>T
XRCC5 transcript	NM_021141.4:c.1834+13262=	NM_021141.4:c.1834+13262C>T
XRCC5 transcript variant X1	XM_005246836.1:c.2119+13262=	XM_005246836.1:c.2119+13262C>T

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#.

77 SubSNP, 20 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	KWOK	ss272205	Jul 12, 2000 (79)
2	SC_JCM	ss819172	Aug 11, 2000 (85)
3	KWOK	ss1128289	Oct 04, 2000 (86)
4	KWOK	ss1231202	Oct 04, 2000 (86)
5	KWOK	ss1801990	Oct 18, 2000 (87)
6	KWOK	ss1841363	Oct 18, 2000 (87)
7	ABI	ss41830248	Mar 15, 2006 (126)
8	EGP_SNPS	ss60198212	Oct 15, 2006 (127)
9	PERLEGEN	ss68842912	May 17, 2007 (127)
10	ILLUMINA	ss75006659	Dec 06, 2007 (129)
11	KRIBB_YJKIM	ss119344282	Dec 01, 2009 (131)
12	COMPLETE_GENOMICS	ss165901999	Jul 04, 2010 (132)
13	COMPLETE_GENOMICS	ss167571552	Jul 04, 2010 (132)
14	ILLUMINA	ss173105790	Jul 04, 2010 (132)
15	1000GENOMES	ss219810184	Jul 14, 2010 (132)
16	1000GENOMES	ss231585090	Jul 14, 2010 (132)
17	BL	ss253874587	May 09, 2011 (134)
18	GMI	ss276896512	May 04, 2012 (137)
19	GMI	ss284541122	Apr 25, 2013 (138)
20	ILLUMINA	ss480066454	May 04, 2012 (137)
21	ILLUMINA	ss484012084	May 04, 2012 (137)
22	ILLUMINA	ss533515963	Sep 08, 2015 (146)
23	SSMP	ss649882791	Apr 25, 2013 (138)
24	ILLUMINA	ss779704163	Sep 08, 2015 (146)
25	ILLUMINA	ss781138408	Sep 08, 2015 (146)
26	ILLUMINA	ss835178364	Sep 08, 2015 (146)
27	EVA-GONL	ss977956915	Aug 21, 2014 (142)
28	JMKIDD_LAB	ss1069938252	Aug 21, 2014 (142)
29	1000GENOMES	ss1301630298	Aug 21, 2014 (142)
30	DDI	ss1428909960	Apr 01, 2015 (144)
31	EVA_GENOME_DK	ss1579321730	Apr 01, 2015 (144)
32	EVA_DECODE	ss1587411702	Apr 01, 2015 (144)
33	EVA_UK10K_ALSPAC	ss1605784426	Apr 01, 2015 (144)
34	EVA_UK10K_TWINSUK	ss1648778459	Apr 01, 2015 (144)
35	EVA_MGP	ss1710995950	Apr 01, 2015 (144)
36	EVA_SVP	ss1712530360	Apr 01, 2015 (144)
37	WEILL_CORNELL_DGM	ss1921201557	Feb 12, 2016 (147)
38	JJLAB	ss2021148926	Sep 14, 2016 (149)
39	USC_VALOUEV	ss2149210358	Dec 20, 2016 (150)
40	HUMAN_LONGEVITY	ss2239119015	Dec 20, 2016 (150)
41	ILLUMINA	ss2633739009	Nov 08, 2017 (151)
42	ILLUMINA	ss2635101035	Nov 08, 2017 (151)
43	GRF	ss2703859119	Nov 08, 2017 (151)
44	GNOMAD	ss2786289505	Nov 08, 2017 (151)
45	SWEGEN	ss2991352298	Nov 08, 2017 (151)
46	BIOINF_KMB_FNS_UNIBA	ss3024332514	Nov 08, 2017 (151)
47	CSHL	ss3344739717	Nov 08, 2017 (151)
48	ILLUMINA	ss3628285067	Oct 11, 2018 (152)
49	ILLUMINA	ss3631699042	Oct 11, 2018 (152)
50	ILLUMINA	ss3638318349	Oct 11, 2018 (152)
51	ILLUMINA	ss3642154965	Oct 11, 2018 (152)
52	ILLUMINA	ss3643283136	Oct 11, 2018 (152)
53	EGCUT_WGS	ss3659247349	Jul 13, 2019 (153)
54	EVA_DECODE	ss3706015249	Jul 13, 2019 (153)
55	ACPOP	ss3729369232	Jul 13, 2019 (153)
56	EVA	ss3758078268	Jul 13, 2019 (153)
57	KHV_HUMAN_GENOMES	ss3802442925	Jul 13, 2019 (153)
58	EVA	ss3827504608	Apr 25, 2020 (154)
59	SGDP_PRJ	ss3854586148	Apr 25, 2020 (154)
60	KRGDB	ss3900304574	Apr 25, 2020 (154)
61	EVA	ss4017049165	Apr 26, 2021 (155)
62	TOPMED	ss4544520302	Apr 26, 2021 (155)
63	TOMMO_GENOMICS	ss5156479508	Apr 26, 2021 (155)
64	1000G_HIGH_COVERAGE	ss5252020624	Oct 12, 2022 (156)
65	EVA	ss5314807781	Oct 12, 2022 (156)
66	EVA	ss5336011021	Oct 12, 2022 (156)
67	HUGCELL_USP	ss5451632424	Oct 12, 2022 (156)
68	EVA	ss5506797090	Oct 12, 2022 (156)
69	1000G_HIGH_COVERAGE	ss5529363369	Oct 12, 2022 (156)
70	SANFORD_IMAGENETICS	ss5630945823	Oct 12, 2022 (156)
71	TOMMO_GENOMICS	ss5687357612	Oct 12, 2022 (156)
72	YY_MCH	ss5803217795	Oct 12, 2022 (156)
73	EVA	ss5821586879	Oct 12, 2022 (156)
74	EVA	ss5852949794	Oct 12, 2022 (156)
75	EVA	ss5934690502	Oct 12, 2022 (156)
76	EVA	ss5957200947	Oct 12, 2022 (156)
77	EVA	ss5980111896	Oct 12, 2022 (156)
78	1000Genomes	NC_000002.11 - 217040033	Oct 11, 2018 (152)
79	1000Genomes_30x	NC_000002.12 - 216175310	Oct 12, 2022 (156)
80	The Avon Longitudinal Study of Parents and Children	NC_000002.11 - 217040033	Oct 11, 2018 (152)
81	Genetic variation in the Estonian population	NC_000002.11 - 217040033	Oct 11, 2018 (152)
82	The Danish reference pan genome	NC_000002.11 - 217040033	Apr 25, 2020 (154)
83	gnomAD - Genomes	NC_000002.12 - 216175310	Apr 26, 2021 (155)
84	Genome of the Netherlands Release 5	NC_000002.11 - 217040033	Apr 25, 2020 (154)
85	HapMap	NC_000002.12 - 216175310	Apr 25, 2020 (154)
86	KOREAN population from KRGDB	NC_000002.11 - 217040033	Apr 25, 2020 (154)
87	Medical Genome Project healthy controls from Spanish population	NC_000002.11 - 217040033	Apr 25, 2020 (154)
88	Northern Sweden	NC_000002.11 - 217040033	Jul 13, 2019 (153)
89	Qatari	NC_000002.11 - 217040033	Apr 25, 2020 (154)
90	SGDP_PRJ	NC_000002.11 - 217040033	Apr 25, 2020 (154)
91	Siberian	NC_000002.11 - 217040033	Apr 25, 2020 (154)
92	8.3KJPN	NC_000002.11 - 217040033	Apr 26, 2021 (155)
93	14KJPN	NC_000002.12 - 216175310	Oct 12, 2022 (156)
94	TopMed	NC_000002.12 - 216175310	Apr 26, 2021 (155)
95	UK 10K study - Twins	NC_000002.11 - 217040033	Oct 11, 2018 (152)
96	A Vietnamese Genetic Variation Database	NC_000002.11 - 217040033	Jul 13, 2019 (153)
97	ALFA	NC_000002.12 - 216175310	Apr 26, 2021 (155)

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)
rs646292	Sep 19, 2000 (85)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss165901999, ss167571552, ss253874587, ss276896512, ss284541122, ss484012084, ss1587411702, ss1712530360, ss2635101035, ss3643283136	NC_000002.10:216748277:C:T	NC_000002.12:216175309:C:T	(self)
12734983, 7041674, 4985597, 5486669, 3089305, 7481968, 112489, 2654097, 3243487, 6603128, 1726712, 14448815, 7041674, 1530639, ss219810184, ss231585090, ss480066454, ss533515963, ss649882791, ss779704163, ss781138408, ss835178364, ss977956915, ss1069938252, ss1301630298, ss1428909960, ss1579321730, ss1605784426, ss1648778459, ss1710995950, ss1921201557, ss2021148926, ss2149210358, ss2633739009, ss2703859119, ss2786289505, ss2991352298, ss3344739717, ss3628285067, ss3631699042, ss3638318349, ss3642154965, ss3659247349, ss3729369232, ss3758078268, ss3827504608, ss3854586148, ss3900304574, ss4017049165, ss5156479508, ss5314807781, ss5336011021, ss5506797090, ss5630945823, ss5821586879, ss5957200947, ss5980111896	NC_000002.11:217040032:C:T	NC_000002.12:216175309:C:T	(self)
16889304, 90820887, 2010244, 21194716, 348343181, 3673097714, ss2239119015, ss3024332514, ss3706015249, ss3802442925, ss4544520302, ss5252020624, ss5451632424, ss5529363369, ss5687357612, ss5803217795, ss5852949794, ss5934690502	NC_000002.12:216175309:C:T	NC_000002.12:216175309:C:T	(self)
ss272205, ss819172, ss1128289, ss1231202, ss1801990, ss1841363, ss41830248, ss60198212, ss68842912, ss75006659, ss119344282, ss173105790	NT_005403.17:67249450:C:T	NC_000002.12:216175309: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 rs207936

PMID	Title	Author	Year	Journal
20463177	Multistudy fine mapping of chromosome 2q identifies XRCC5 as a chronic obstructive pulmonary disease susceptibility gene.	Hersh CP et al.	2010	American journal of respiratory and critical care medicine

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.

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dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs207936