Name: rs1320744
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.

rs1320744

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:189932898 (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=0.005418 (1434/264690, TOPMED)
T=0.004999 (701/140230, GnomAD)
T=0.00431 (152/35246, ALFA) (+ 15 more)
T=0.03284 (928/28256, 14KJPN)
T=0.03371 (565/16760, 8.3KJPN)
T=0.0123 (79/6404, 1000G_30x)
T=0.0126 (63/5008, 1000G)
T=0.0025 (11/4480, Estonian)
T=0.0078 (30/3854, ALSPAC)
T=0.0040 (15/3708, TWINSUK)
T=0.0024 (7/2922, KOREAN)
T=0.0022 (4/1832, Korea1K)
T=0.003 (3/998, GoNL)
T=0.000 (0/304, HapMap)
T=0.005 (1/216, Qatari)
T=0.014 (3/214, Vietnamese)
C=0.5 (5/10, SGDP_PRJ)
T=0.5 (5/10, SGDP_PRJ)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: None
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	35246	C=0.99569	T=0.00431
European	Sub	30370	C=0.99595	T=0.00405
African	Sub	2946	C=0.9949	T=0.0051
African Others	Sub	114	C=0.991	T=0.009
African American	Sub	2832	C=0.9951	T=0.0049
Asian	Sub	156	C=1.000	T=0.000
East Asian	Sub	130	C=1.000	T=0.000
Other Asian	Sub	26	C=1.00	T=0.00
Latin American 1	Sub	146	C=0.993	T=0.007
Latin American 2	Sub	610	C=0.990	T=0.010
South Asian	Sub	98	C=1.00	T=0.00
Other	Sub	920	C=0.992	T=0.008

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=0.994582	T=0.005418
gnomAD - Genomes	Global	Study-wide	140230	C=0.995001	T=0.004999
gnomAD - Genomes	European	Sub	75920	C=0.99535	T=0.00465
gnomAD - Genomes	African	Sub	42052	C=0.99501	T=0.00499
gnomAD - Genomes	American	Sub	13650	C=0.99267	T=0.00733
gnomAD - Genomes	Ashkenazi Jewish	Sub	3320	C=0.9994	T=0.0006
gnomAD - Genomes	East Asian	Sub	3134	C=0.9968	T=0.0032
gnomAD - Genomes	Other	Sub	2154	C=0.9879	T=0.0121
Allele Frequency Aggregator	Total	Global	35246	C=0.99569	T=0.00431
Allele Frequency Aggregator	European	Sub	30370	C=0.99595	T=0.00405
Allele Frequency Aggregator	African	Sub	2946	C=0.9949	T=0.0051
Allele Frequency Aggregator	Other	Sub	920	C=0.992	T=0.008
Allele Frequency Aggregator	Latin American 2	Sub	610	C=0.990	T=0.010
Allele Frequency Aggregator	Asian	Sub	156	C=1.000	T=0.000
Allele Frequency Aggregator	Latin American 1	Sub	146	C=0.993	T=0.007
Allele Frequency Aggregator	South Asian	Sub	98	C=1.00	T=0.00
14KJPN	JAPANESE	Study-wide	28256	C=0.96716	T=0.03284
8.3KJPN	JAPANESE	Study-wide	16760	C=0.96629	T=0.03371
1000Genomes_30x	Global	Study-wide	6404	C=0.9877	T=0.0123
1000Genomes_30x	African	Sub	1786	C=0.9950	T=0.0050
1000Genomes_30x	Europe	Sub	1266	C=0.9929	T=0.0071
1000Genomes_30x	South Asian	Sub	1202	C=0.9667	T=0.0333
1000Genomes_30x	East Asian	Sub	1170	C=0.9897	T=0.0103
1000Genomes_30x	American	Sub	980	C=0.991	T=0.009
1000Genomes	Global	Study-wide	5008	C=0.9874	T=0.0126
1000Genomes	African	Sub	1322	C=0.9947	T=0.0053
1000Genomes	East Asian	Sub	1008	C=0.9881	T=0.0119
1000Genomes	Europe	Sub	1006	C=0.9950	T=0.0050
1000Genomes	South Asian	Sub	978	C=0.966	T=0.034
1000Genomes	American	Sub	694	C=0.991	T=0.009
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.9975	T=0.0025
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.9922	T=0.0078
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.9960	T=0.0040
KOREAN population from KRGDB	KOREAN	Study-wide	2922	C=0.9976	T=0.0024
Korean Genome Project	KOREAN	Study-wide	1832	C=0.9978	T=0.0022
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.997	T=0.003
HapMap	Global	Study-wide	304	C=1.000	T=0.000
HapMap	American	Sub	116	C=1.000	T=0.000
HapMap	African	Sub	106	C=1.000	T=0.000
HapMap	Asian	Sub	82	C=1.00	T=0.00
Qatari	Global	Study-wide	216	C=0.995	T=0.005
A Vietnamese Genetic Variation Database	Global	Study-wide	214	C=0.986	T=0.014
SGDP_PRJ	Global	Study-wide	10	C=0.5	T=0.5

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.189932898C>T
GRCh37.p13 chr 1	NC_000001.10:g.189902028C>T

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 1	NC_000001.11:g.189932898=	NC_000001.11:g.189932898C>T
GRCh37.p13 chr 1	NC_000001.10:g.189902028=	NC_000001.10:g.189902028C>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#.

36 SubSNP, 17 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	TSC-CSHL	ss2089173	Oct 23, 2000 (88)
2	SC_JCM	ss5639785	Feb 20, 2003 (111)
3	ABI	ss44027680	Mar 13, 2006 (126)
4	1000GENOMES	ss329105882	May 09, 2011 (134)
5	SSMP	ss648576340	Apr 25, 2013 (138)
6	EVA-GONL	ss975942086	Aug 21, 2014 (142)
7	JMKIDD_LAB	ss1068459339	Aug 21, 2014 (142)
8	1000GENOMES	ss1293907302	Aug 21, 2014 (142)
9	EVA_DECODE	ss1585335291	Apr 01, 2015 (144)
10	EVA_UK10K_ALSPAC	ss1601738205	Apr 01, 2015 (144)
11	EVA_UK10K_TWINSUK	ss1644732238	Apr 01, 2015 (144)
12	HAMMER_LAB	ss1795459242	Sep 08, 2015 (146)
13	WEILL_CORNELL_DGM	ss1919177030	Feb 12, 2016 (147)
14	HUMAN_LONGEVITY	ss2168555343	Dec 20, 2016 (150)
15	ILLUMINA	ss2710688871	Nov 08, 2017 (151)
16	GNOMAD	ss2764096204	Nov 08, 2017 (151)
17	SWEGEN	ss2988146442	Nov 08, 2017 (151)
18	EGCUT_WGS	ss3656100261	Jul 12, 2019 (153)
19	EVA_DECODE	ss3688259487	Jul 12, 2019 (153)
20	EVA	ss3747107135	Jul 12, 2019 (153)
21	KHV_HUMAN_GENOMES	ss3800111763	Jul 12, 2019 (153)
22	SGDP_PRJ	ss3850513143	Apr 25, 2020 (154)
23	KRGDB	ss3895781787	Apr 25, 2020 (154)
24	KOGIC	ss3946128095	Apr 25, 2020 (154)
25	TOPMED	ss4476962750	Apr 25, 2021 (155)
26	TOMMO_GENOMICS	ss5147584689	Apr 25, 2021 (155)
27	1000G_HIGH_COVERAGE	ss5245145646	Oct 12, 2022 (156)
28	EVA	ss5323605715	Oct 12, 2022 (156)
29	HUGCELL_USP	ss5445645379	Oct 12, 2022 (156)
30	1000G_HIGH_COVERAGE	ss5518908353	Oct 12, 2022 (156)
31	SANFORD_IMAGENETICS	ss5627078307	Oct 12, 2022 (156)
32	TOMMO_GENOMICS	ss5675100109	Oct 12, 2022 (156)
33	EVA	ss5833001370	Oct 12, 2022 (156)
34	EVA	ss5849206901	Oct 12, 2022 (156)
35	EVA	ss5911226596	Oct 12, 2022 (156)
36	EVA	ss5938897856	Oct 12, 2022 (156)
37	1000Genomes	NC_000001.10 - 189902028	Oct 11, 2018 (152)
38	1000Genomes_30x	NC_000001.11 - 189932898	Oct 12, 2022 (156)
39	The Avon Longitudinal Study of Parents and Children	NC_000001.10 - 189902028	Oct 11, 2018 (152)
40	Genetic variation in the Estonian population	NC_000001.10 - 189902028	Oct 11, 2018 (152)
41	gnomAD - Genomes	NC_000001.11 - 189932898	Apr 25, 2021 (155)
42	Genome of the Netherlands Release 5	NC_000001.10 - 189902028	Apr 25, 2020 (154)
43	HapMap	NC_000001.11 - 189932898	Apr 25, 2020 (154)
44	KOREAN population from KRGDB	NC_000001.10 - 189902028	Apr 25, 2020 (154)
45	Korean Genome Project	NC_000001.11 - 189932898	Apr 25, 2020 (154)
46	Qatari	NC_000001.10 - 189902028	Apr 25, 2020 (154)
47	SGDP_PRJ	NC_000001.10 - 189902028	Apr 25, 2020 (154)
48	8.3KJPN	NC_000001.10 - 189902028	Apr 25, 2021 (155)
49	14KJPN	NC_000001.11 - 189932898	Oct 12, 2022 (156)
50	TopMed	NC_000001.11 - 189932898	Apr 25, 2021 (155)
51	UK 10K study - Twins	NC_000001.10 - 189902028	Oct 11, 2018 (152)
52	A Vietnamese Genetic Variation Database	NC_000001.10 - 189902028	Jul 12, 2019 (153)
53	ALFA	NC_000001.11 - 189932898	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).

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss1585335291	NC_000001.9:188168650:C:T	NC_000001.11:189932897:C:T	(self)
4734511, 2596869, 1838509, 1130926, 2959181, 1218960, 2530123, 5553996, 2596869, 558895, ss329105882, ss648576340, ss975942086, ss1068459339, ss1293907302, ss1601738205, ss1644732238, ss1795459242, ss1919177030, ss2710688871, ss2764096204, ss2988146442, ss3656100261, ss3747107135, ss3850513143, ss3895781787, ss5147584689, ss5323605715, ss5627078307, ss5833001370, ss5938897856	NC_000001.10:189902027:C:T	NC_000001.11:189932897:C:T	(self)
6434288, 34133010, 227811, 2506096, 8937213, 40569085, 5320393120, ss2168555343, ss3688259487, ss3800111763, ss3946128095, ss4476962750, ss5245145646, ss5445645379, ss5518908353, ss5675100109, ss5849206901, ss5911226596	NC_000001.11:189932897:C:T	NC_000001.11:189932897:C:T	(self)
ss2089173, ss5639785, ss44027680	NT_004487.19:41390669:C:T	NC_000001.11:189932897: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 rs1320744

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

rs1320744