Name: rs5759668
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.

rs5759668

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr22:23264197 (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=0.216200 (57226/264690, TOPMED)
T=0.209226 (29321/140140, GnomAD)
T=0.06384 (1804/28258, 14KJPN) (+ 18 more)
T=0.15729 (3942/25062, ALFA)
T=0.06390 (1071/16760, 8.3KJPN)
T=0.2080 (1332/6404, 1000G_30x)
T=0.2019 (1011/5008, 1000G)
T=0.0781 (301/3854, ALSPAC)
T=0.0793 (294/3708, TWINSUK)
T=0.0708 (207/2922, KOREAN)
T=0.0584 (107/1832, Korea1K)
T=0.080 (80/998, GoNL)
T=0.233 (146/626, Chileans)
T=0.105 (63/600, NorthernSweden)
T=0.094 (50/534, MGP)
T=0.236 (51/216, Qatari)
T=0.033 (7/214, Vietnamese)
C=0.337 (58/172, SGDP_PRJ)
T=0.25 (10/40, GENOME_DK)
C=0.50 (6/12, Siberian)
T=0.50 (6/12, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: BCR : Intron Variant
FBXW4P1 : Non Coding Transcript 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	25062	C=0.84271	T=0.15729
European	Sub	17436	C=0.90560	T=0.09440
African	Sub	3658	C=0.5331	T=0.4669
African Others	Sub	126	C=0.516	T=0.484
African American	Sub	3532	C=0.5337	T=0.4663
Asian	Sub	164	C=0.921	T=0.079
East Asian	Sub	104	C=0.962	T=0.038
Other Asian	Sub	60	C=0.85	T=0.15
Latin American 1	Sub	258	C=0.826	T=0.174
Latin American 2	Sub	1902	C=0.8517	T=0.1483
South Asian	Sub	110	C=0.955	T=0.045
Other	Sub	1534	C=0.8416	T=0.1584

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=0.783800	T=0.216200
gnomAD - Genomes	Global	Study-wide	140140	C=0.790774	T=0.209226
gnomAD - Genomes	European	Sub	75936	C=0.91175	T=0.08825
gnomAD - Genomes	African	Sub	41950	C=0.53502	T=0.46498
gnomAD - Genomes	American	Sub	13660	C=0.82980	T=0.17020
gnomAD - Genomes	Ashkenazi Jewish	Sub	3322	C=0.9241	T=0.0759
gnomAD - Genomes	East Asian	Sub	3126	C=0.9447	T=0.0553
gnomAD - Genomes	Other	Sub	2146	C=0.8304	T=0.1696
14KJPN	JAPANESE	Study-wide	28258	C=0.93616	T=0.06384
Allele Frequency Aggregator	Total	Global	25062	C=0.84271	T=0.15729
Allele Frequency Aggregator	European	Sub	17436	C=0.90560	T=0.09440
Allele Frequency Aggregator	African	Sub	3658	C=0.5331	T=0.4669
Allele Frequency Aggregator	Latin American 2	Sub	1902	C=0.8517	T=0.1483
Allele Frequency Aggregator	Other	Sub	1534	C=0.8416	T=0.1584
Allele Frequency Aggregator	Latin American 1	Sub	258	C=0.826	T=0.174
Allele Frequency Aggregator	Asian	Sub	164	C=0.921	T=0.079
Allele Frequency Aggregator	South Asian	Sub	110	C=0.955	T=0.045
8.3KJPN	JAPANESE	Study-wide	16760	C=0.93610	T=0.06390
1000Genomes_30x	Global	Study-wide	6404	C=0.7920	T=0.2080
1000Genomes_30x	African	Sub	1786	C=0.4882	T=0.5118
1000Genomes_30x	Europe	Sub	1266	C=0.9226	T=0.0774
1000Genomes_30x	South Asian	Sub	1202	C=0.9509	T=0.0491
1000Genomes_30x	East Asian	Sub	1170	C=0.9171	T=0.0829
1000Genomes_30x	American	Sub	980	C=0.833	T=0.167
1000Genomes	Global	Study-wide	5008	C=0.7981	T=0.2019
1000Genomes	African	Sub	1322	C=0.4796	T=0.5204
1000Genomes	East Asian	Sub	1008	C=0.9266	T=0.0734
1000Genomes	Europe	Sub	1006	C=0.9215	T=0.0785
1000Genomes	South Asian	Sub	978	C=0.951	T=0.049
1000Genomes	American	Sub	694	C=0.824	T=0.176
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.9219	T=0.0781
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.9207	T=0.0793
KOREAN population from KRGDB	KOREAN	Study-wide	2922	C=0.9292	T=0.0708
Korean Genome Project	KOREAN	Study-wide	1832	C=0.9416	T=0.0584
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.920	T=0.080
Chileans	Chilean	Study-wide	626	C=0.767	T=0.233
Northern Sweden	ACPOP	Study-wide	600	C=0.895	T=0.105
Medical Genome Project healthy controls from Spanish population	Spanish controls	Study-wide	534	C=0.906	T=0.094
Qatari	Global	Study-wide	216	C=0.764	T=0.236
A Vietnamese Genetic Variation Database	Global	Study-wide	214	C=0.967	T=0.033
SGDP_PRJ	Global	Study-wide	172	C=0.337	T=0.663
The Danish reference pan genome	Danish	Study-wide	40	C=0.75	T=0.25
Siberian	Global	Study-wide	12	C=0.50	T=0.50

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.23264197C>T
GRCh37.p13 chr 22	NC_000022.10:g.23606384C>T
BCR RefSeqGene (LRG_1112)	NG_009244.2:g.88833C>T

Gene: BCR, BCR activator of RhoGEF and GTPase (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
BCR transcript variant 1	NM_004327.4:c.1752+2657C>T	N/A	Intron Variant
BCR transcript variant 2	NM_021574.3:c.1752+2657C>T	N/A	Intron Variant

Gene: FBXW4P1, F-box and WD repeat domain containing 4 pseudogene 1 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
FBXW4P1 transcript	NR_033408.1:n.1431C>T	N/A	Non Coding 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.

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 22	NC_000022.11:g.23264197=	NC_000022.11:g.23264197C>T
GRCh37.p13 chr 22	NC_000022.10:g.23606384=	NC_000022.10:g.23606384C>T
BCR RefSeqGene (LRG_1112)	NG_009244.2:g.88833=	NG_009244.2:g.88833C>T
FBXW4P1 transcript	NR_033408.1:n.1431=	NR_033408.1:n.1431C>T
FBXW3 transcript	NM_012165.1:c.1059=	NM_012165.1:c.1059C>T
BCR transcript variant 1	NM_004327.3:c.1752+2657=	NM_004327.3:c.1752+2657C>T
BCR transcript variant 1	NM_004327.4:c.1752+2657=	NM_004327.4:c.1752+2657C>T
BCR transcript variant 2	NM_021574.2:c.1752+2657=	NM_021574.2:c.1752+2657C>T
BCR transcript variant 2	NM_021574.3:c.1752+2657=	NM_021574.3:c.1752+2657C>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#.

61 SubSNP, 20 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	WI_SSAHASNP	ss12524369	Jul 11, 2003 (117)
2	SC_SNP	ss15449781	Feb 27, 2004 (120)
3	CSHL-HAPMAP	ss20140016	Feb 27, 2004 (120)
4	PERLEGEN	ss38338806	May 24, 2005 (125)
5	AFFY	ss66262271	Nov 30, 2006 (127)
6	AFFY	ss76407324	Dec 08, 2007 (129)
7	KRIBB_YJKIM	ss82185335	Dec 16, 2007 (130)
8	AFFY	ss173494666	Jul 04, 2010 (132)
9	BUSHMAN	ss204058156	Jul 04, 2010 (132)
10	1000GENOMES	ss228630323	Jul 14, 2010 (132)
11	1000GENOMES	ss238031403	Jul 15, 2010 (132)
12	1000GENOMES	ss244159239	Jul 15, 2010 (132)
13	PJP	ss292741274	May 09, 2011 (134)
14	ILLUMINA	ss535858326	Sep 08, 2015 (146)
15	TISHKOFF	ss566575943	Apr 25, 2013 (138)
16	SSMP	ss662503725	Apr 25, 2013 (138)
17	EVA-GONL	ss995247552	Aug 21, 2014 (142)
18	JMKIDD_LAB	ss1082586681	Aug 21, 2014 (142)
19	1000GENOMES	ss1366782558	Aug 21, 2014 (142)
20	EVA_GENOME_DK	ss1579713902	Apr 01, 2015 (144)
21	EVA_UK10K_ALSPAC	ss1639796765	Apr 01, 2015 (144)
22	EVA_UK10K_TWINSUK	ss1682790798	Apr 01, 2015 (144)
23	EVA_DECODE	ss1699316163	Apr 01, 2015 (144)
24	EVA_MGP	ss1711563173	Apr 01, 2015 (144)
25	EVA_SVP	ss1713733025	Apr 01, 2015 (144)
26	HAMMER_LAB	ss1809745037	Sep 08, 2015 (146)
27	WEILL_CORNELL_DGM	ss1938813147	Feb 12, 2016 (147)
28	JJLAB	ss2030179230	Sep 14, 2016 (149)
29	USC_VALOUEV	ss2158791032	Dec 20, 2016 (150)
30	GRF	ss2704538570	Nov 08, 2017 (151)
31	GNOMAD	ss2973302012	Nov 08, 2017 (151)
32	SWEGEN	ss3019141821	Nov 08, 2017 (151)
33	BIOINF_KMB_FNS_UNIBA	ss3028926947	Nov 08, 2017 (151)
34	CSHL	ss3352790699	Nov 08, 2017 (151)
35	ILLUMINA	ss3628510570	Oct 12, 2018 (152)
36	OMUKHERJEE_ADBS	ss3646564224	Oct 12, 2018 (152)
37	EVA_DECODE	ss3708002398	Jul 13, 2019 (153)
38	ACPOP	ss3743845921	Jul 13, 2019 (153)
39	EVA	ss3759261223	Jul 13, 2019 (153)
40	PACBIO	ss3788800712	Jul 13, 2019 (153)
41	PACBIO	ss3793670892	Jul 13, 2019 (153)
42	PACBIO	ss3798557258	Jul 13, 2019 (153)
43	KHV_HUMAN_GENOMES	ss3822428367	Jul 13, 2019 (153)
44	EVA	ss3825966875	Apr 27, 2020 (154)
45	SGDP_PRJ	ss3890336244	Apr 27, 2020 (154)
46	KRGDB	ss3940726004	Apr 27, 2020 (154)
47	KOGIC	ss3983444362	Apr 27, 2020 (154)
48	TOPMED	ss5105896071	Apr 27, 2021 (155)
49	TOMMO_GENOMICS	ss5232177740	Apr 27, 2021 (155)
50	1000G_HIGH_COVERAGE	ss5310757040	Oct 16, 2022 (156)
51	EVA	ss5440691134	Oct 16, 2022 (156)
52	HUGCELL_USP	ss5502639041	Oct 16, 2022 (156)
53	EVA	ss5512352502	Oct 16, 2022 (156)
54	1000G_HIGH_COVERAGE	ss5618157783	Oct 16, 2022 (156)
55	SANFORD_IMAGENETICS	ss5664299789	Oct 16, 2022 (156)
56	TOMMO_GENOMICS	ss5793158341	Oct 16, 2022 (156)
57	YY_MCH	ss5818623243	Oct 16, 2022 (156)
58	EVA	ss5821936304	Oct 16, 2022 (156)
59	EVA	ss5881440159	Oct 16, 2022 (156)
60	EVA	ss5959154267	Oct 16, 2022 (156)
61	EVA	ss5981321261	Oct 16, 2022 (156)
62	1000Genomes	NC_000022.10 - 23606384	Oct 12, 2018 (152)
63	1000Genomes_30x	NC_000022.11 - 23264197	Oct 16, 2022 (156)
64	The Avon Longitudinal Study of Parents and Children	NC_000022.10 - 23606384	Oct 12, 2018 (152)
65	Chileans	NC_000022.10 - 23606384	Apr 27, 2020 (154)
66	The Danish reference pan genome	NC_000022.10 - 23606384	Apr 27, 2020 (154)
67	gnomAD - Genomes	NC_000022.11 - 23264197	Apr 27, 2021 (155)
68	Genome of the Netherlands Release 5	NC_000022.10 - 23606384	Apr 27, 2020 (154)
69	KOREAN population from KRGDB	NC_000022.10 - 23606384	Apr 27, 2020 (154)
70	Korean Genome Project	NC_000022.11 - 23264197	Apr 27, 2020 (154)
71	Medical Genome Project healthy controls from Spanish population	NC_000022.10 - 23606384	Apr 27, 2020 (154)
72	Northern Sweden	NC_000022.10 - 23606384	Jul 13, 2019 (153)
73	Qatari	NC_000022.10 - 23606384	Apr 27, 2020 (154)
74	SGDP_PRJ	NC_000022.10 - 23606384	Apr 27, 2020 (154)
75	Siberian	NC_000022.10 - 23606384	Apr 27, 2020 (154)
76	8.3KJPN	NC_000022.10 - 23606384	Apr 27, 2021 (155)
77	14KJPN	NC_000022.11 - 23264197	Oct 16, 2022 (156)
78	TopMed	NC_000022.11 - 23264197	Apr 27, 2021 (155)
79	UK 10K study - Twins	NC_000022.10 - 23606384	Oct 12, 2018 (152)
80	A Vietnamese Genetic Variation Database	NC_000022.10 - 23606384	Jul 13, 2019 (153)
81	ALFA	NC_000022.11 - 23264197	Apr 27, 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)
rs8137860	Aug 27, 2003 (117)
rs61247787	Feb 27, 2009 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss204058156, ss292741274, ss1699316163, ss1713733025	NC_000022.9:21936383:C:T	NC_000022.11:23264196:C:T	(self)
80320326, 44429532, 268495, 5878841, 19796509, 47903398, 678933, 17130786, 20855069, 42353224, 11307386, 90147047, 44429532, 9803793, ss228630323, ss238031403, ss244159239, ss535858326, ss566575943, ss662503725, ss995247552, ss1082586681, ss1366782558, ss1579713902, ss1639796765, ss1682790798, ss1711563173, ss1809745037, ss1938813147, ss2030179230, ss2158791032, ss2704538570, ss2973302012, ss3019141821, ss3352790699, ss3628510570, ss3646564224, ss3743845921, ss3759261223, ss3788800712, ss3793670892, ss3798557258, ss3825966875, ss3890336244, ss3940726004, ss5232177740, ss5440691134, ss5512352502, ss5664299789, ss5821936304, ss5959154267, ss5981321261	NC_000022.10:23606383:C:T	NC_000022.11:23264196:C:T	(self)
105683718, 567233948, 39822363, 126995445, 381005018, 7491176180, ss3028926947, ss3708002398, ss3822428367, ss3983444362, ss5105896071, ss5310757040, ss5502639041, ss5618157783, ss5793158341, ss5818623243, ss5881440159	NC_000022.11:23264196:C:T	NC_000022.11:23264196:C:T	(self)
ss12524369, ss20140016	NT_011520.9:2996952:C:T	NC_000022.11:23264196:C:T	(self)
ss15449781, ss38338806, ss66262271, ss76407324, ss82185335, ss173494666	NT_011520.12:2996952:C:T	NC_000022.11:23264196:C:T	(self)

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

No publications for rs5759668

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

rs5759668