Name: rs1320758
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.

rs1320758

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:247618923 (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: A>C / A>T
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.425528 (112633/264690, TOPMED)
T=0.437304 (61205/139960, GnomAD)
T=0.42352 (11967/28256, 14KJPN) (+ 17 more)
T=0.43081 (8138/18890, ALFA)
T=0.42267 (7084/16760, 8.3KJPN)
T=0.4143 (2653/6404, 1000G_30x)
T=0.4095 (2051/5008, 1000G)
T=0.4196 (1880/4480, Estonian)
T=0.4318 (1664/3854, ALSPAC)
T=0.4266 (1582/3708, TWINSUK)
T=0.3976 (1165/2930, KOREAN)
T=0.4138 (758/1832, Korea1K)
T=0.435 (434/998, GoNL)
T=0.472 (283/600, NorthernSweden)
A=0.349 (118/338, SGDP_PRJ)
T=0.439 (143/326, HapMap)
T=0.333 (72/216, Qatari)
T=0.425 (90/212, Vietnamese)
T=0.40 (16/40, GENOME_DK)
A=0.37 (11/30, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: OR14L1P : Intron Variant
LOC102724446 : 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	18890	A=0.56919	T=0.43081
European	Sub	14286	A=0.56678	T=0.43322
African	Sub	2946	A=0.5411	T=0.4589
African Others	Sub	114	A=0.404	T=0.596
African American	Sub	2832	A=0.5466	T=0.4534
Asian	Sub	112	A=0.598	T=0.402
East Asian	Sub	86	A=0.60	T=0.40
Other Asian	Sub	26	A=0.58	T=0.42
Latin American 1	Sub	146	A=0.521	T=0.479
Latin American 2	Sub	610	A=0.707	T=0.293
South Asian	Sub	98	A=0.74	T=0.26
Other	Sub	692	A=0.598	T=0.402

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	A=0.574472	T=0.425528
gnomAD - Genomes	Global	Study-wide	139960	A=0.562696	T=0.437304
gnomAD - Genomes	European	Sub	75820	A=0.56488	T=0.43512
gnomAD - Genomes	African	Sub	41936	A=0.53415	T=0.46585
gnomAD - Genomes	American	Sub	13624	A=0.64739	T=0.35261
gnomAD - Genomes	Ashkenazi Jewish	Sub	3322	A=0.5412	T=0.4588
gnomAD - Genomes	East Asian	Sub	3104	A=0.5567	T=0.4433
gnomAD - Genomes	Other	Sub	2154	A=0.5478	T=0.4522
14KJPN	JAPANESE	Study-wide	28256	A=0.57648	T=0.42352
Allele Frequency Aggregator	Total	Global	18890	A=0.56919	T=0.43081
Allele Frequency Aggregator	European	Sub	14286	A=0.56678	T=0.43322
Allele Frequency Aggregator	African	Sub	2946	A=0.5411	T=0.4589
Allele Frequency Aggregator	Other	Sub	692	A=0.598	T=0.402
Allele Frequency Aggregator	Latin American 2	Sub	610	A=0.707	T=0.293
Allele Frequency Aggregator	Latin American 1	Sub	146	A=0.521	T=0.479
Allele Frequency Aggregator	Asian	Sub	112	A=0.598	T=0.402
Allele Frequency Aggregator	South Asian	Sub	98	A=0.74	T=0.26
8.3KJPN	JAPANESE	Study-wide	16760	A=0.57733	T=0.42267
1000Genomes_30x	Global	Study-wide	6404	A=0.5857	T=0.4143
1000Genomes_30x	African	Sub	1786	A=0.5017	T=0.4983
1000Genomes_30x	Europe	Sub	1266	A=0.5537	T=0.4463
1000Genomes_30x	South Asian	Sub	1202	A=0.6872	T=0.3128
1000Genomes_30x	East Asian	Sub	1170	A=0.5803	T=0.4197
1000Genomes_30x	American	Sub	980	A=0.662	T=0.338
1000Genomes	Global	Study-wide	5008	A=0.5905	T=0.4095
1000Genomes	African	Sub	1322	A=0.5106	T=0.4894
1000Genomes	East Asian	Sub	1008	A=0.5724	T=0.4276
1000Genomes	Europe	Sub	1006	A=0.5586	T=0.4414
1000Genomes	South Asian	Sub	978	A=0.694	T=0.306
1000Genomes	American	Sub	694	A=0.669	T=0.331
Genetic variation in the Estonian population	Estonian	Study-wide	4480	A=0.5804	T=0.4196
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.5682	T=0.4318
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.5734	T=0.4266
KOREAN population from KRGDB	KOREAN	Study-wide	2930	A=0.6024	C=0.0000, T=0.3976
Korean Genome Project	KOREAN	Study-wide	1832	A=0.5862	T=0.4138
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	A=0.565	T=0.435
Northern Sweden	ACPOP	Study-wide	600	A=0.528	T=0.472
SGDP_PRJ	Global	Study-wide	338	A=0.349	T=0.651
HapMap	Global	Study-wide	326	A=0.561	T=0.439
HapMap	African	Sub	120	A=0.525	T=0.475
HapMap	American	Sub	118	A=0.568	T=0.432
HapMap	Asian	Sub	88	A=0.60	T=0.40
Qatari	Global	Study-wide	216	A=0.667	T=0.333
A Vietnamese Genetic Variation Database	Global	Study-wide	212	A=0.575	T=0.425
The Danish reference pan genome	Danish	Study-wide	40	A=0.60	T=0.40
Siberian	Global	Study-wide	30	A=0.37	T=0.63

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.247618923A>C
GRCh38.p14 chr 1	NC_000001.11:g.247618923A>T
GRCh37.p13 chr 1	NC_000001.10:g.247782225A>C
GRCh37.p13 chr 1	NC_000001.10:g.247782225A>T

Gene: OR14L1P, olfactory receptor family 14 subfamily L member 1 pseudogene (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
OR14L1 transcript	NM_001396106.1:c.38-699A>C	N/A	Intron Variant

Gene: LOC102724446, uncharacterized LOC102724446 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC102724446 transcript	XR_426948.4: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	A=	C	T
GRCh38.p14 chr 1	NC_000001.11:g.247618923=	NC_000001.11:g.247618923A>C	NC_000001.11:g.247618923A>T
GRCh37.p13 chr 1	NC_000001.10:g.247782225=	NC_000001.10:g.247782225A>C	NC_000001.10:g.247782225A>T
OR14L1 transcript	NM_001396106.1:c.38-699=	NM_001396106.1:c.38-699A>C	NM_001396106.1:c.38-699A>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#.

79 SubSNP, 20 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	TSC-CSHL	ss2089189	Oct 23, 2000 (88)
2	WI_SSAHASNP	ss6810034	Feb 20, 2003 (111)
3	CSHL-HAPMAP	ss17370430	Feb 27, 2004 (120)
4	CSHL-HAPMAP	ss19867206	Feb 27, 2004 (120)
5	SSAHASNP	ss20504698	Apr 05, 2004 (121)
6	PERLEGEN	ss24325922	Sep 20, 2004 (123)
7	ABI	ss44092220	Mar 14, 2006 (126)
8	PERLEGEN	ss68800645	May 17, 2007 (127)
9	HGSV	ss86043062	Dec 15, 2007 (130)
10	BGI	ss102843115	Dec 01, 2009 (131)
11	1000GENOMES	ss112117623	Jan 25, 2009 (130)
12	ENSEMBL	ss161240201	Dec 01, 2009 (131)
13	COMPLETE_GENOMICS	ss165640406	Jul 04, 2010 (132)
14	COMPLETE_GENOMICS	ss167597967	Jul 04, 2010 (132)
15	BUSHMAN	ss199906249	Jul 04, 2010 (132)
16	BCM-HGSC-SUB	ss205179564	Jul 04, 2010 (132)
17	1000GENOMES	ss219006683	Jul 14, 2010 (132)
18	1000GENOMES	ss230996214	Jul 14, 2010 (132)
19	1000GENOMES	ss238590993	Jul 15, 2010 (132)
20	BL	ss253949933	May 09, 2011 (134)
21	GMI	ss276311261	May 04, 2012 (137)
22	PJP	ss290789851	May 09, 2011 (134)
23	ILLUMINA	ss482299107	May 04, 2012 (137)
24	ILLUMINA	ss483866273	May 04, 2012 (137)
25	ILLUMINA	ss536061763	Sep 08, 2015 (146)
26	TISHKOFF	ss555288689	Apr 25, 2013 (138)
27	SSMP	ss648864270	Apr 25, 2013 (138)
28	ILLUMINA	ss780437891	Aug 21, 2014 (142)
29	ILLUMINA	ss782376717	Aug 21, 2014 (142)
30	ILLUMINA	ss835927508	Aug 21, 2014 (142)
31	EVA-GONL	ss976385485	Aug 21, 2014 (142)
32	JMKIDD_LAB	ss1068783004	Aug 21, 2014 (142)
33	1000GENOMES	ss1295534508	Aug 21, 2014 (142)
34	DDI	ss1426185182	Apr 01, 2015 (144)
35	EVA_GENOME_DK	ss1574834201	Apr 01, 2015 (144)
36	EVA_DECODE	ss1585788466	Apr 01, 2015 (144)
37	EVA_UK10K_ALSPAC	ss1602609474	Apr 01, 2015 (144)
38	EVA_UK10K_TWINSUK	ss1645603507	Apr 01, 2015 (144)
39	HAMMER_LAB	ss1796089891	Sep 08, 2015 (146)
40	WEILL_CORNELL_DGM	ss1919609754	Feb 12, 2016 (147)
41	GENOMED	ss1967031948	Jul 19, 2016 (147)
42	JJLAB	ss2020333239	Sep 14, 2016 (149)
43	USC_VALOUEV	ss2148372949	Dec 20, 2016 (150)
44	HUMAN_LONGEVITY	ss2171872781	Dec 20, 2016 (150)
45	SYSTEMSBIOZJU	ss2624681089	Nov 08, 2017 (151)
46	ILLUMINA	ss2632660287	Nov 08, 2017 (151)
47	GRF	ss2698380460	Nov 08, 2017 (151)
48	GNOMAD	ss2768696413	Nov 08, 2017 (151)
49	SWEGEN	ss2988822068	Nov 08, 2017 (151)
50	BIOINF_KMB_FNS_UNIBA	ss3023930115	Nov 08, 2017 (151)
51	CSHL	ss3344023824	Nov 08, 2017 (151)
52	ILLUMINA	ss3626362096	Oct 11, 2018 (152)
53	ILLUMINA	ss3630688655	Oct 11, 2018 (152)
54	ILLUMINA	ss3641654591	Oct 11, 2018 (152)
55	EGCUT_WGS	ss3656777953	Jul 12, 2019 (153)
56	EVA_DECODE	ss3689075523	Jul 12, 2019 (153)
57	ACPOP	ss3728066534	Jul 12, 2019 (153)
58	EVA	ss3747615517	Jul 12, 2019 (153)
59	KHV_HUMAN_GENOMES	ss3800619825	Jul 12, 2019 (153)
60	EVA	ss3826766990	Apr 25, 2020 (154)
61	EVA	ss3836787494	Apr 25, 2020 (154)
62	EVA	ss3842200908	Apr 25, 2020 (154)
63	SGDP_PRJ	ss3851373982	Apr 25, 2020 (154)
64	KRGDB	ss3896743703	Apr 25, 2020 (154)
65	KOGIC	ss3946928813	Apr 25, 2020 (154)
66	TOPMED	ss4491146278	Apr 25, 2021 (155)
67	TOMMO_GENOMICS	ss5149447903	Apr 25, 2021 (155)
68	1000G_HIGH_COVERAGE	ss5246578737	Oct 12, 2022 (156)
69	EVA	ss5314701967	Oct 12, 2022 (156)
70	EVA	ss5326200552	Oct 12, 2022 (156)
71	HUGCELL_USP	ss5446935661	Oct 12, 2022 (156)
72	1000G_HIGH_COVERAGE	ss5521054455	Oct 12, 2022 (156)
73	SANFORD_IMAGENETICS	ss5627898107	Oct 12, 2022 (156)
74	TOMMO_GENOMICS	ss5677502547	Oct 12, 2022 (156)
75	YY_MCH	ss5801842351	Oct 12, 2022 (156)
76	EVA	ss5833582070	Oct 12, 2022 (156)
77	EVA	ss5849389220	Oct 12, 2022 (156)
78	EVA	ss5912858939	Oct 12, 2022 (156)
79	EVA	ss5939747080	Oct 12, 2022 (156)
80	1000Genomes	NC_000001.10 - 247782225	Oct 11, 2018 (152)
81	1000Genomes_30x	NC_000001.11 - 247618923	Oct 12, 2022 (156)
82	The Avon Longitudinal Study of Parents and Children	NC_000001.10 - 247782225	Oct 11, 2018 (152)
83	Genetic variation in the Estonian population	NC_000001.10 - 247782225	Oct 11, 2018 (152)
84	The Danish reference pan genome	NC_000001.10 - 247782225	Apr 25, 2020 (154)
85	gnomAD - Genomes	NC_000001.11 - 247618923	Apr 25, 2021 (155)
86	Genome of the Netherlands Release 5	NC_000001.10 - 247782225	Apr 25, 2020 (154)
87	HapMap	NC_000001.11 - 247618923	Apr 25, 2020 (154)
88	KOREAN population from KRGDB	NC_000001.10 - 247782225	Apr 25, 2020 (154)
89	Korean Genome Project	NC_000001.11 - 247618923	Apr 25, 2020 (154)
90	Northern Sweden	NC_000001.10 - 247782225	Jul 12, 2019 (153)
91	Qatari	NC_000001.10 - 247782225	Apr 25, 2020 (154)
92	SGDP_PRJ	NC_000001.10 - 247782225	Apr 25, 2020 (154)
93	Siberian	NC_000001.10 - 247782225	Apr 25, 2020 (154)
94	8.3KJPN	NC_000001.10 - 247782225	Apr 25, 2021 (155)
95	14KJPN	NC_000001.11 - 247618923	Oct 12, 2022 (156)
96	TopMed	NC_000001.11 - 247618923	Apr 25, 2021 (155)
97	UK 10K study - Twins	NC_000001.10 - 247782225	Oct 11, 2018 (152)
98	A Vietnamese Genetic Variation Database	NC_000001.10 - 247782225	Jul 12, 2019 (153)
99	ALFA	NC_000001.11 - 247618923	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)
rs17319372	Oct 07, 2004 (123)
rs58882974	May 25, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
3921097, ss3896743703	NC_000001.10:247782224:A:C	NC_000001.11:247618922:A:C	(self)
ss86043062	NC_000001.8:244108265:A:T	NC_000001.11:247618922:A:T	(self)
ss112117623, ss165640406, ss167597967, ss199906249, ss205179564, ss253949933, ss276311261, ss290789851, ss482299107, ss1585788466	NC_000001.9:245848847:A:T	NC_000001.11:247618922:A:T	(self)
6422477, 3557494, 2516201, 1983157, 1561569, 3921097, 1351399, 1651684, 3390962, 889303, 7417210, 3557494, 776311, ss219006683, ss230996214, ss238590993, ss483866273, ss536061763, ss555288689, ss648864270, ss780437891, ss782376717, ss835927508, ss976385485, ss1068783004, ss1295534508, ss1426185182, ss1574834201, ss1602609474, ss1645603507, ss1796089891, ss1919609754, ss1967031948, ss2020333239, ss2148372949, ss2624681089, ss2632660287, ss2698380460, ss2768696413, ss2988822068, ss3344023824, ss3626362096, ss3630688655, ss3641654591, ss3656777953, ss3728066534, ss3747615517, ss3826766990, ss3836787494, ss3851373982, ss3896743703, ss5149447903, ss5314701967, ss5326200552, ss5627898107, ss5833582070, ss5939747080	NC_000001.10:247782224:A:T	NC_000001.11:247618922:A:T	(self)
8580390, 45869907, 315741, 3306814, 11339651, 54752613, 14972967406, ss2171872781, ss3023930115, ss3689075523, ss3800619825, ss3842200908, ss3946928813, ss4491146278, ss5246578737, ss5446935661, ss5521054455, ss5677502547, ss5801842351, ss5849389220, ss5912858939	NC_000001.11:247618922:A:T	NC_000001.11:247618922:A:T	(self)
ss17370430, ss19867206, ss20504698	NT_004836.15:12445588:A:T	NC_000001.11:247618922:A:T	(self)
ss2089189, ss6810034, ss24325922, ss44092220, ss68800645, ss102843115, ss161240201	NT_167186.1:41300003:A:T	NC_000001.11:247618922:A: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 rs1320758

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

rs1320758