Name: rs4245756
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.

rs4245756

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:864083 (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: T>C
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.027572 (7298/264690, TOPMED)
T=0.026157 (3668/140232, GnomAD)
T=0.00000 (0/28258, 14KJPN) (+ 16 more)
T=0.02276 (587/25796, ALFA)
T=0.00000 (0/16760, 8.3KJPN)
T=0.0312 (200/6404, 1000G_30x)
T=0.0276 (138/5008, 1000G)
T=0.0018 (7/3854, ALSPAC)
T=0.0022 (8/3708, TWINSUK)
T=0.0000 (0/2930, KOREAN)
T=0.0000 (0/1832, Korea1K)
T=0.0445 (49/1100, HapMap)
T=0.001 (1/998, GoNL)
T=0.002 (1/600, NorthernSweden)
T=0.007 (4/558, SGDP_PRJ)
T=0.014 (3/216, Qatari)
T=0.000 (0/216, Vietnamese)
T=0.00 (0/56, Siberian)
T=0.00 (0/40, GENOME_DK)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: LOC107984850 : 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	25796	T=0.02276	C=0.97724
European	Sub	15678	T=0.00089	C=0.99911
African	Sub	7392	T=0.0729	C=0.9271
African Others	Sub	240	T=0.062	C=0.938
African American	Sub	7152	T=0.0733	C=0.9267
Asian	Sub	164	T=0.000	C=1.000
East Asian	Sub	104	T=0.000	C=1.000
Other Asian	Sub	60	T=0.00	C=1.00
Latin American 1	Sub	220	T=0.050	C=0.950
Latin American 2	Sub	760	T=0.007	C=0.993
South Asian	Sub	110	T=0.000	C=1.000
Other	Sub	1472	T=0.0122	C=0.9878

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	T=0.027572	C=0.972428
gnomAD - Genomes	Global	Study-wide	140232	T=0.026157	C=0.973843
gnomAD - Genomes	European	Sub	75960	T=0.00118	C=0.99882
gnomAD - Genomes	African	Sub	42002	T=0.08023	C=0.91977
gnomAD - Genomes	American	Sub	13660	T=0.01105	C=0.98895
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	T=0.0003	C=0.9997
gnomAD - Genomes	East Asian	Sub	3132	T=0.0000	C=1.0000
gnomAD - Genomes	Other	Sub	2154	T=0.0260	C=0.9740
14KJPN	JAPANESE	Study-wide	28258	T=0.00000	C=1.00000
Allele Frequency Aggregator	Total	Global	25796	T=0.02276	C=0.97724
Allele Frequency Aggregator	European	Sub	15678	T=0.00089	C=0.99911
Allele Frequency Aggregator	African	Sub	7392	T=0.0729	C=0.9271
Allele Frequency Aggregator	Other	Sub	1472	T=0.0122	C=0.9878
Allele Frequency Aggregator	Latin American 2	Sub	760	T=0.007	C=0.993
Allele Frequency Aggregator	Latin American 1	Sub	220	T=0.050	C=0.950
Allele Frequency Aggregator	Asian	Sub	164	T=0.000	C=1.000
Allele Frequency Aggregator	South Asian	Sub	110	T=0.000	C=1.000
8.3KJPN	JAPANESE	Study-wide	16760	T=0.00000	C=1.00000
1000Genomes_30x	Global	Study-wide	6404	T=0.0312	C=0.9688
1000Genomes_30x	African	Sub	1786	T=0.1053	C=0.8947
1000Genomes_30x	Europe	Sub	1266	T=0.0016	C=0.9984
1000Genomes_30x	South Asian	Sub	1202	T=0.0000	C=1.0000
1000Genomes_30x	East Asian	Sub	1170	T=0.0000	C=1.0000
1000Genomes_30x	American	Sub	980	T=0.010	C=0.990
1000Genomes	Global	Study-wide	5008	T=0.0276	C=0.9724
1000Genomes	African	Sub	1322	T=0.0983	C=0.9017
1000Genomes	East Asian	Sub	1008	T=0.0000	C=1.0000
1000Genomes	Europe	Sub	1006	T=0.0010	C=0.9990
1000Genomes	South Asian	Sub	978	T=0.000	C=1.000
1000Genomes	American	Sub	694	T=0.010	C=0.990
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.0018	C=0.9982
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.0022	C=0.9978
KOREAN population from KRGDB	KOREAN	Study-wide	2930	T=0.0000	C=1.0000
Korean Genome Project	KOREAN	Study-wide	1832	T=0.0000	C=1.0000
HapMap	Global	Study-wide	1100	T=0.0445	C=0.9555
HapMap	African	Sub	692	T=0.058	C=0.942
HapMap	American	Sub	318	T=0.028	C=0.972
HapMap	Asian	Sub	90	T=0.00	C=1.00
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.001	C=0.999
Northern Sweden	ACPOP	Study-wide	600	T=0.002	C=0.998
SGDP_PRJ	Global	Study-wide	558	T=0.007	C=0.993
Qatari	Global	Study-wide	216	T=0.014	C=0.986
A Vietnamese Genetic Variation Database	Global	Study-wide	216	T=0.000	C=1.000
Siberian	Global	Study-wide	56	T=0.00	C=1.00
The Danish reference pan genome	Danish	Study-wide	40	T=0.00	C=1.00

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 1	NC_000001.11:g.864083T>C
GRCh37.p13 chr 1	NC_000001.10:g.799463T>C

Gene: LOC107984850, uncharacterized LOC107984850 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC107984850 transcript variant X1	XR_001737607.3:n.	N/A	Intron Variant
LOC107984850 transcript variant X2	XR_001737608.3:n.	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	T=	C
GRCh38.p14 chr 1	NC_000001.11:g.864083=	NC_000001.11:g.864083T>C
GRCh37.p13 chr 1	NC_000001.10:g.799463=	NC_000001.10:g.799463T>C

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#.

88 SubSNP, 19 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_JCM	ss6064692	Feb 20, 2003 (111)
2	WI_SSAHASNP	ss6851739	Feb 20, 2003 (111)
3	BCM_SSAHASNP	ss9857255	Jul 11, 2003 (117)
4	SC_SNP	ss15431649	Feb 27, 2004 (120)
5	CSHL-HAPMAP	ss16443054	Feb 27, 2004 (120)
6	SSAHASNP	ss20429617	Apr 05, 2004 (121)
7	AFFY	ss66174584	Nov 30, 2006 (127)
8	ILLUMINA	ss75246605	Dec 06, 2007 (129)
9	AFFY	ss76232689	Dec 08, 2007 (130)
10	HGSV	ss78658745	Dec 06, 2007 (129)
11	KRIBB_YJKIM	ss82006065	Dec 15, 2007 (130)
12	HGSV	ss84000839	Dec 14, 2007 (130)
13	HGSV	ss85801006	Dec 14, 2007 (130)
14	BCMHGSC_JDW	ss87156111	Mar 23, 2008 (129)
15	HUMANGENOME_JCVI	ss97913268	Feb 04, 2009 (130)
16	BGI	ss105111729	Dec 01, 2009 (131)
17	1000GENOMES	ss107938292	Jan 22, 2009 (130)
18	ILLUMINA-UK	ss118438430	Feb 14, 2009 (130)
19	ENSEMBL	ss131814903	Dec 01, 2009 (131)
20	ENSEMBL	ss137752346	Dec 01, 2009 (131)
21	GMI	ss154522467	Dec 01, 2009 (131)
22	AFFY	ss172905536	Jul 04, 2010 (132)
23	ILLUMINA	ss173702064	Jul 04, 2010 (132)
24	BUSHMAN	ss197885519	Jul 04, 2010 (132)
25	BCM-HGSC-SUB	ss205195537	Jul 04, 2010 (132)
26	1000GENOMES	ss218190491	Jul 14, 2010 (132)
27	1000GENOMES	ss230395508	Jul 14, 2010 (132)
28	1000GENOMES	ss238115028	Jul 15, 2010 (132)
29	BL	ss252864188	May 09, 2011 (134)
30	GMI	ss275680967	May 04, 2012 (137)
31	GMI	ss283987424	Apr 25, 2013 (138)
32	PJP	ss290493830	May 09, 2011 (134)
33	ILLUMINA	ss537221257	Sep 08, 2015 (146)
34	TISHKOFF	ss553710667	Apr 25, 2013 (138)
35	SSMP	ss647516445	Apr 25, 2013 (138)
36	EVA-GONL	ss974769612	Aug 21, 2014 (142)
37	JMKIDD_LAB	ss1067612431	Aug 21, 2014 (142)
38	1000GENOMES	ss1289340279	Aug 21, 2014 (142)
39	DDI	ss1425684945	Apr 01, 2015 (144)
40	EVA_GENOME_DK	ss1573851216	Apr 01, 2015 (144)
41	EVA_DECODE	ss1584129644	Apr 01, 2015 (144)
42	EVA_UK10K_ALSPAC	ss1599378557	Apr 01, 2015 (144)
43	EVA_UK10K_TWINSUK	ss1642372590	Apr 01, 2015 (144)
44	EVA_SVP	ss1712305468	Apr 01, 2015 (144)
45	HAMMER_LAB	ss1793706225	Sep 08, 2015 (146)
46	WEILL_CORNELL_DGM	ss1917960785	Feb 12, 2016 (147)
47	GENOMED	ss1966667362	Jul 19, 2016 (147)
48	JJLAB	ss2019498496	Sep 14, 2016 (149)
49	USC_VALOUEV	ss2147484471	Dec 20, 2016 (150)
50	SYSTEMSBIOZJU	ss2624264827	Nov 08, 2017 (151)
51	GRF	ss2697374862	Nov 08, 2017 (151)
52	GNOMAD	ss2750641718	Nov 08, 2017 (151)
53	SWEGEN	ss2986149494	Nov 08, 2017 (151)
54	CSHL	ss3343272695	Nov 08, 2017 (151)
55	ILLUMINA	ss3626006539	Oct 11, 2018 (152)
56	ILLUMINA	ss3637732371	Oct 11, 2018 (152)
57	ILLUMINA	ss3640973134	Oct 11, 2018 (152)
58	ILLUMINA	ss3641266950	Oct 11, 2018 (152)
59	ILLUMINA	ss3642746674	Oct 11, 2018 (152)
60	URBANLAB	ss3646581268	Oct 11, 2018 (152)
61	EVA_DECODE	ss3685992513	Jul 12, 2019 (153)
62	ACPOP	ss3726716528	Jul 12, 2019 (153)
63	EVA	ss3745721203	Jul 12, 2019 (153)
64	PACBIO	ss3783302198	Jul 12, 2019 (153)
65	PACBIO	ss3788980067	Jul 12, 2019 (153)
66	PACBIO	ss3793852604	Jul 12, 2019 (153)
67	KHV_HUMAN_GENOMES	ss3798743874	Jul 12, 2019 (153)
68	EVA	ss3825981517	Apr 25, 2020 (154)
69	EVA	ss3836378469	Apr 25, 2020 (154)
70	EVA	ss3841782472	Apr 25, 2020 (154)
71	SGDP_PRJ	ss3847996167	Apr 25, 2020 (154)
72	KRGDB	ss3892836422	Apr 25, 2020 (154)
73	KOGIC	ss3943630117	Apr 25, 2020 (154)
74	EVA	ss4016889043	Apr 25, 2021 (155)
75	TOPMED	ss4436440310	Apr 25, 2021 (155)
76	TOMMO_GENOMICS	ss5142053376	Apr 25, 2021 (155)
77	1000G_HIGH_COVERAGE	ss5240864366	Oct 12, 2022 (156)
78	EVA	ss5316184682	Oct 12, 2022 (156)
79	HUGCELL_USP	ss5442112649	Oct 12, 2022 (156)
80	1000G_HIGH_COVERAGE	ss5512489384	Oct 12, 2022 (156)
81	SANFORD_IMAGENETICS	ss5624749982	Oct 12, 2022 (156)
82	TOMMO_GENOMICS	ss5666192990	Oct 12, 2022 (156)
83	YY_MCH	ss5800244007	Oct 12, 2022 (156)
84	EVA	ss5831418732	Oct 12, 2022 (156)
85	EVA	ss5848748912	Oct 12, 2022 (156)
86	EVA	ss5906705287	Oct 12, 2022 (156)
87	EVA	ss5936583060	Oct 12, 2022 (156)
88	EVA	ss5979926039	Oct 12, 2022 (156)
89	1000Genomes	NC_000001.10 - 799463	Oct 11, 2018 (152)
90	1000Genomes_30x	NC_000001.11 - 864083	Oct 12, 2022 (156)
91	The Avon Longitudinal Study of Parents and Children	NC_000001.10 - 799463	Oct 11, 2018 (152)
92	The Danish reference pan genome	NC_000001.10 - 799463	Apr 25, 2020 (154)
93	gnomAD - Genomes	NC_000001.11 - 864083	Apr 25, 2021 (155)
94	Genome of the Netherlands Release 5	NC_000001.10 - 799463	Apr 25, 2020 (154)
95	HapMap	NC_000001.11 - 864083	Apr 25, 2020 (154)
96	KOREAN population from KRGDB	NC_000001.10 - 799463	Apr 25, 2020 (154)
97	Korean Genome Project	NC_000001.11 - 864083	Apr 25, 2020 (154)
98	Northern Sweden	NC_000001.10 - 799463	Jul 12, 2019 (153)
99	Qatari	NC_000001.10 - 799463	Apr 25, 2020 (154)
100	SGDP_PRJ	NC_000001.10 - 799463	Apr 25, 2020 (154)
101	Siberian	NC_000001.10 - 799463	Apr 25, 2020 (154)
102	8.3KJPN	NC_000001.10 - 799463	Apr 25, 2021 (155)
103	14KJPN	NC_000001.11 - 864083	Oct 12, 2022 (156)
104	TopMed	NC_000001.11 - 864083	Apr 25, 2021 (155)
105	UK 10K study - Twins	NC_000001.10 - 799463	Oct 11, 2018 (152)
106	A Vietnamese Genetic Variation Database	NC_000001.10 - 799463	Jul 12, 2019 (153)
107	ALFA	NC_000001.11 - 864083	Apr 25, 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)
rs6680444	Aug 27, 2003 (117)
rs56538647	May 24, 2008 (130)
rs58071205	May 24, 2008 (130)
rs59004701	Feb 26, 2009 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss78658745, ss84000839, ss85801006	NC_000001.8:839325:T:C	NC_000001.11:864082:T:C	(self)
ss66174584, ss76232689, ss87156111, ss107938292, ss118438430, ss172905536, ss197885519, ss205195537, ss252864188, ss275680967, ss283987424, ss290493830, ss1584129644, ss1712305468, ss3642746674	NC_000001.9:789325:T:C	NC_000001.11:864082:T:C	(self)
5047, 522, 1358450, 639, 13816, 1393, 2715, 13147, 825, 22683, 522, 109, ss218190491, ss230395508, ss238115028, ss537221257, ss553710667, ss647516445, ss974769612, ss1067612431, ss1289340279, ss1425684945, ss1573851216, ss1599378557, ss1642372590, ss1793706225, ss1917960785, ss1966667362, ss2019498496, ss2147484471, ss2624264827, ss2697374862, ss2750641718, ss2986149494, ss3343272695, ss3626006539, ss3637732371, ss3640973134, ss3641266950, ss3726716528, ss3745721203, ss3783302198, ss3788980067, ss3793852604, ss3825981517, ss3836378469, ss3847996167, ss3892836422, ss4016889043, ss5142053376, ss5316184682, ss5624749982, ss5831418732, ss5936583060, ss5979926039	NC_000001.10:799462:T:C	NC_000001.11:864082:T:C	(self)
15319, 71468, 85, 8118, 30094, 46645, 1329698393, ss3646581268, ss3685992513, ss3798743874, ss3841782472, ss3943630117, ss4436440310, ss5240864366, ss5442112649, ss5512489384, ss5666192990, ss5800244007, ss5848748912, ss5906705287	NC_000001.11:864082:T:C	NC_000001.11:864082:T:C	(self)
ss6064692, ss6851739, ss75246605, ss82006065, ss97913268, ss105111729, ss131814903, ss137752346, ss154522467, ss173702064	NT_004350.19:278094:T:C	NC_000001.11:864082:T:C	(self)
ss9857255, ss15431649, ss16443054, ss20429617	NT_034471.3:278094:T:C	NC_000001.11:864082:T:C	(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 rs4245756

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

rs4245756