Name: rs12891892
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.

rs12891892

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr14:50052108 (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>A / C>G
Variation Type: SNV Single Nucleotide Variation
Frequency: A=0.254275 (67304/264690, TOPMED)
A=0.262130 (36705/140026, GnomAD)
A=0.24734 (19464/78692, PAGE_STUDY) (+ 20 more)
A=0.30371 (11174/36792, ALFA)
C=0.47940 (13547/28258, 14KJPN)
C=0.48132 (8067/16760, 8.3KJPN)
A=0.2890 (1851/6404, 1000G_30x)
A=0.2947 (1476/5008, 1000G)
A=0.4480 (2007/4480, Estonian)
A=0.3295 (1270/3854, ALSPAC)
A=0.3417 (1267/3708, TWINSUK)
A=0.4853 (1422/2930, KOREAN)
A=0.2484 (470/1892, HapMap)
A=0.4847 (888/1832, Korea1K)
A=0.339 (338/998, GoNL)
A=0.423 (265/626, Chileans)
A=0.367 (220/600, NorthernSweden)
C=0.321 (95/296, SGDP_PRJ)
A=0.148 (32/216, Qatari)
C=0.466 (97/208, Vietnamese)
A=0.18 (12/66, Ancient Sardinia)
C=0.29 (14/48, Siberian)
A=0.25 (10/40, GENOME_DK)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: LINC01599 : 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	36792	C=0.69629	A=0.30371
European	Sub	28660	C=0.65939	A=0.34061
African	Sub	4746	C=0.9309	A=0.0691
African Others	Sub	158	C=0.994	A=0.006
African American	Sub	4588	C=0.9287	A=0.0713
Asian	Sub	170	C=0.476	A=0.524
East Asian	Sub	142	C=0.472	A=0.528
Other Asian	Sub	28	C=0.50	A=0.50
Latin American 1	Sub	182	C=0.813	A=0.187
Latin American 2	Sub	754	C=0.562	A=0.438
South Asian	Sub	120	C=0.658	A=0.342
Other	Sub	2160	C=0.7269	A=0.2731

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=0.745725	A=0.254275
gnomAD - Genomes	Global	Study-wide	140026	C=0.737870	A=0.262130
gnomAD - Genomes	European	Sub	75826	C=0.65088	A=0.34912
gnomAD - Genomes	African	Sub	41984	C=0.93133	A=0.06867
gnomAD - Genomes	American	Sub	13624	C=0.67029	A=0.32971
gnomAD - Genomes	Ashkenazi Jewish	Sub	3320	C=0.7934	A=0.2066
gnomAD - Genomes	East Asian	Sub	3122	C=0.4926	A=0.5074
gnomAD - Genomes	Other	Sub	2150	C=0.7265	A=0.2735
The PAGE Study	Global	Study-wide	78692	C=0.75266	A=0.24734
The PAGE Study	AfricanAmerican	Sub	32514	C=0.92536	A=0.07464
The PAGE Study	Mexican	Sub	10810	C=0.54727	A=0.45273
The PAGE Study	Asian	Sub	8316	C=0.4965	A=0.5035
The PAGE Study	PuertoRican	Sub	7914	C=0.7703	A=0.2297
The PAGE Study	NativeHawaiian	Sub	4532	C=0.5391	A=0.4609
The PAGE Study	Cuban	Sub	4230	C=0.7492	A=0.2508
The PAGE Study	Dominican	Sub	3828	C=0.8312	A=0.1688
The PAGE Study	CentralAmerican	Sub	2450	C=0.6302	A=0.3698
The PAGE Study	SouthAmerican	Sub	1982	C=0.6367	A=0.3633
The PAGE Study	NativeAmerican	Sub	1260	C=0.6659	A=0.3341
The PAGE Study	SouthAsian	Sub	856	C=0.655	A=0.345
Allele Frequency Aggregator	Total	Global	36792	C=0.69629	A=0.30371
Allele Frequency Aggregator	European	Sub	28660	C=0.65939	A=0.34061
Allele Frequency Aggregator	African	Sub	4746	C=0.9309	A=0.0691
Allele Frequency Aggregator	Other	Sub	2160	C=0.7269	A=0.2731
Allele Frequency Aggregator	Latin American 2	Sub	754	C=0.562	A=0.438
Allele Frequency Aggregator	Latin American 1	Sub	182	C=0.813	A=0.187
Allele Frequency Aggregator	Asian	Sub	170	C=0.476	A=0.524
Allele Frequency Aggregator	South Asian	Sub	120	C=0.658	A=0.342
14KJPN	JAPANESE	Study-wide	28258	C=0.47940	A=0.52060
8.3KJPN	JAPANESE	Study-wide	16760	C=0.48132	A=0.51868
1000Genomes_30x	Global	Study-wide	6404	C=0.7110	A=0.2890
1000Genomes_30x	African	Sub	1786	C=0.9782	A=0.0218
1000Genomes_30x	Europe	Sub	1266	C=0.6714	A=0.3286
1000Genomes_30x	South Asian	Sub	1202	C=0.6547	A=0.3453
1000Genomes_30x	East Asian	Sub	1170	C=0.4752	A=0.5248
1000Genomes_30x	American	Sub	980	C=0.626	A=0.374
1000Genomes	Global	Study-wide	5008	C=0.7053	A=0.2947
1000Genomes	African	Sub	1322	C=0.9781	A=0.0219
1000Genomes	East Asian	Sub	1008	C=0.4792	A=0.5208
1000Genomes	Europe	Sub	1006	C=0.6670	A=0.3330
1000Genomes	South Asian	Sub	978	C=0.653	A=0.347
1000Genomes	American	Sub	694	C=0.643	A=0.357
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.5520	A=0.4480
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.6705	A=0.3295
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.6583	A=0.3417
KOREAN population from KRGDB	KOREAN	Study-wide	2930	C=0.5147	A=0.4853, G=0.0000
HapMap	Global	Study-wide	1892	C=0.7516	A=0.2484
HapMap	American	Sub	770	C=0.638	A=0.362
HapMap	African	Sub	692	C=0.984	A=0.016
HapMap	Asian	Sub	254	C=0.480	A=0.520
HapMap	Europe	Sub	176	C=0.727	A=0.273
Korean Genome Project	KOREAN	Study-wide	1832	C=0.5153	A=0.4847
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.661	A=0.339
Chileans	Chilean	Study-wide	626	C=0.577	A=0.423
Northern Sweden	ACPOP	Study-wide	600	C=0.633	A=0.367
SGDP_PRJ	Global	Study-wide	296	C=0.321	A=0.679
Qatari	Global	Study-wide	216	C=0.852	A=0.148
A Vietnamese Genetic Variation Database	Global	Study-wide	208	C=0.466	A=0.534
Ancient Sardinia genome-wide 1240k capture data generation and analysis	Global	Study-wide	66	C=0.82	A=0.18
Siberian	Global	Study-wide	48	C=0.29	A=0.71
The Danish reference pan genome	Danish	Study-wide	40	C=0.75	A=0.25

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 14	NC_000014.9:g.50052108C>A
GRCh38.p14 chr 14	NC_000014.9:g.50052108C>G
GRCh37.p13 chr 14	NC_000014.8:g.50518826C>A
GRCh37.p13 chr 14	NC_000014.8:g.50518826C>G

Gene: LINC01599, long intergenic non-protein coding RNA 1599 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LINC01599 transcript	NR_131171.1: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	C=	A	G
GRCh38.p14 chr 14	NC_000014.9:g.50052108=	NC_000014.9:g.50052108C>A	NC_000014.9:g.50052108C>G
GRCh37.p13 chr 14	NC_000014.8:g.50518826=	NC_000014.8:g.50518826C>A	NC_000014.8:g.50518826C>G

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, 23 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SSAHASNP	ss21204271	Apr 05, 2004 (121)
2	ABI	ss43579504	Mar 15, 2006 (126)
3	PERLEGEN	ss69156677	May 17, 2007 (127)
4	ILLUMINA	ss75078421	Dec 06, 2007 (129)
5	HGSV	ss77480989	Dec 06, 2007 (129)
6	HUMANGENOME_JCVI	ss96916711	Feb 06, 2009 (130)
7	BGI	ss103184638	Dec 01, 2009 (131)
8	1000GENOMES	ss108327345	Jan 23, 2009 (130)
9	KRIBB_YJKIM	ss119815676	Dec 01, 2009 (131)
10	ENSEMBL	ss132323211	Dec 01, 2009 (131)
11	COMPLETE_GENOMICS	ss171088040	Jul 04, 2010 (132)
12	ILLUMINA	ss172268317	Jul 04, 2010 (132)
13	1000GENOMES	ss236536159	Jul 15, 2010 (132)
14	1000GENOMES	ss242971512	Jul 15, 2010 (132)
15	BL	ss254972434	May 09, 2011 (134)
16	GMI	ss281997742	May 04, 2012 (137)
17	GMI	ss286839149	Apr 25, 2013 (138)
18	PJP	ss291598464	May 09, 2011 (134)
19	ILLUMINA	ss479160605	May 04, 2012 (137)
20	ILLUMINA	ss483299504	May 04, 2012 (137)
21	ILLUMINA	ss532756562	Sep 08, 2015 (146)
22	SSMP	ss659760995	Apr 25, 2013 (138)
23	ILLUMINA	ss779534869	Sep 08, 2015 (146)
24	ILLUMINA	ss780912228	Sep 08, 2015 (146)
25	ILLUMINA	ss835005485	Sep 08, 2015 (146)
26	EVA-GONL	ss991132521	Aug 21, 2014 (142)
27	JMKIDD_LAB	ss1079644004	Aug 21, 2014 (142)
28	1000GENOMES	ss1350954316	Aug 21, 2014 (142)
29	DDI	ss1427419173	Apr 01, 2015 (144)
30	EVA_GENOME_DK	ss1577246868	Apr 01, 2015 (144)
31	EVA_UK10K_ALSPAC	ss1631706484	Apr 01, 2015 (144)
32	EVA_UK10K_TWINSUK	ss1674700517	Apr 01, 2015 (144)
33	EVA_DECODE	ss1695130181	Apr 01, 2015 (144)
34	EVA_SVP	ss1713443078	Apr 01, 2015 (144)
35	WEILL_CORNELL_DGM	ss1934508819	Feb 12, 2016 (147)
36	ILLUMINA	ss1959553558	Feb 12, 2016 (147)
37	GENOMED	ss1967959219	Jul 19, 2016 (147)
38	JJLAB	ss2028030960	Sep 14, 2016 (149)
39	USC_VALOUEV	ss2156404910	Dec 20, 2016 (150)
40	HUMAN_LONGEVITY	ss2201879075	Dec 20, 2016 (150)
41	SYSTEMSBIOZJU	ss2628504663	Nov 08, 2017 (151)
42	ILLUMINA	ss2633148417	Nov 08, 2017 (151)
43	GRF	ss2700828031	Nov 08, 2017 (151)
44	GNOMAD	ss2927559498	Nov 08, 2017 (151)
45	SWEGEN	ss3012181625	Nov 08, 2017 (151)
46	ILLUMINA	ss3021567698	Nov 08, 2017 (151)
47	BIOINF_KMB_FNS_UNIBA	ss3027839992	Nov 08, 2017 (151)
48	CSHL	ss3350800095	Nov 08, 2017 (151)
49	ILLUMINA	ss3627214665	Oct 12, 2018 (152)
50	ILLUMINA	ss3631146565	Oct 12, 2018 (152)
51	ILLUMINA	ss3638049422	Oct 12, 2018 (152)
52	ILLUMINA	ss3641876805	Oct 12, 2018 (152)
53	ILLUMINA	ss3643036177	Oct 12, 2018 (152)
54	URBANLAB	ss3650204604	Oct 12, 2018 (152)
55	ILLUMINA	ss3651960426	Oct 12, 2018 (152)
56	EGCUT_WGS	ss3679428924	Jul 13, 2019 (153)
57	EVA_DECODE	ss3696653272	Jul 13, 2019 (153)
58	ILLUMINA	ss3725446567	Jul 13, 2019 (153)
59	ACPOP	ss3740370532	Jul 13, 2019 (153)
60	EVA	ss3752305339	Jul 13, 2019 (153)
61	PAGE_CC	ss3771787832	Jul 13, 2019 (153)
62	PACBIO	ss3787661058	Jul 13, 2019 (153)
63	PACBIO	ss3792700544	Jul 13, 2019 (153)
64	PACBIO	ss3797584691	Jul 13, 2019 (153)
65	KHV_HUMAN_GENOMES	ss3817639977	Jul 13, 2019 (153)
66	EVA	ss3833912152	Apr 27, 2020 (154)
67	EVA	ss3840549085	Apr 27, 2020 (154)
68	EVA	ss3846037922	Apr 27, 2020 (154)
69	SGDP_PRJ	ss3881481099	Apr 27, 2020 (154)
70	KRGDB	ss3930490100	Apr 27, 2020 (154)
71	KOGIC	ss3974901841	Apr 27, 2020 (154)
72	EVA	ss3985678530	Apr 26, 2021 (155)
73	EVA	ss4017669186	Apr 26, 2021 (155)
74	TOPMED	ss4970224507	Apr 26, 2021 (155)
75	TOMMO_GENOMICS	ss5213176892	Apr 26, 2021 (155)
76	1000G_HIGH_COVERAGE	ss5296179724	Oct 16, 2022 (156)
77	EVA	ss5315735406	Oct 16, 2022 (156)
78	EVA	ss5415187634	Oct 16, 2022 (156)
79	HUGCELL_USP	ss5490227405	Oct 16, 2022 (156)
80	1000G_HIGH_COVERAGE	ss5596445316	Oct 16, 2022 (156)
81	SANFORD_IMAGENETICS	ss5656197323	Oct 16, 2022 (156)
82	TOMMO_GENOMICS	ss5765962921	Oct 16, 2022 (156)
83	YY_MCH	ss5814740730	Oct 16, 2022 (156)
84	EVA	ss5841090177	Oct 16, 2022 (156)
85	EVA	ss5851026534	Oct 16, 2022 (156)
86	EVA	ss5901288037	Oct 16, 2022 (156)
87	EVA	ss5947624206	Oct 16, 2022 (156)
88	EVA	ss5980826145	Oct 16, 2022 (156)
89	1000Genomes	NC_000014.8 - 50518826	Oct 12, 2018 (152)
90	1000Genomes_30x	NC_000014.9 - 50052108	Oct 16, 2022 (156)
91	The Avon Longitudinal Study of Parents and Children	NC_000014.8 - 50518826	Oct 12, 2018 (152)
92	Chileans	NC_000014.8 - 50518826	Apr 27, 2020 (154)
93	Genetic variation in the Estonian population	NC_000014.8 - 50518826	Oct 12, 2018 (152)
94	The Danish reference pan genome	NC_000014.8 - 50518826	Apr 27, 2020 (154)
95	gnomAD - Genomes	NC_000014.9 - 50052108	Apr 26, 2021 (155)
96	Genome of the Netherlands Release 5	NC_000014.8 - 50518826	Apr 27, 2020 (154)
97	HapMap	NC_000014.9 - 50052108	Apr 27, 2020 (154)
98	KOREAN population from KRGDB	NC_000014.8 - 50518826	Apr 27, 2020 (154)
99	Korean Genome Project	NC_000014.9 - 50052108	Apr 27, 2020 (154)
100	Northern Sweden	NC_000014.8 - 50518826	Jul 13, 2019 (153)
101	The PAGE Study	NC_000014.9 - 50052108	Jul 13, 2019 (153)
102	Ancient Sardinia genome-wide 1240k capture data generation and analysis	NC_000014.8 - 50518826	Apr 26, 2021 (155)
103	Qatari	NC_000014.8 - 50518826	Apr 27, 2020 (154)
104	SGDP_PRJ	NC_000014.8 - 50518826	Apr 27, 2020 (154)
105	Siberian	NC_000014.8 - 50518826	Apr 27, 2020 (154)
106	8.3KJPN	NC_000014.8 - 50518826	Apr 26, 2021 (155)
107	14KJPN	NC_000014.9 - 50052108	Oct 16, 2022 (156)
108	TopMed	NC_000014.9 - 50052108	Apr 26, 2021 (155)
109	UK 10K study - Twins	NC_000014.8 - 50518826	Oct 12, 2018 (152)
110	A Vietnamese Genetic Variation Database	NC_000014.8 - 50518826	Jul 13, 2019 (153)
111	ALFA	NC_000014.9 - 50052108	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).

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss77480989, ss108327345, ss171088040, ss254972434, ss281997742, ss286839149, ss291598464, ss483299504, ss1695130181, ss1713443078, ss3643036177	NC_000014.7:49588575:C:A	NC_000014.9:50052107:C:A	(self)
63932957, 35511897, 137515, 25167172, 3598198, 15863846, 37667494, 13655397, 904457, 16550749, 33498079, 8921264, 71146199, 35511897, 7900632, ss236536159, ss242971512, ss479160605, ss532756562, ss659760995, ss779534869, ss780912228, ss835005485, ss991132521, ss1079644004, ss1350954316, ss1427419173, ss1577246868, ss1631706484, ss1674700517, ss1934508819, ss1959553558, ss1967959219, ss2028030960, ss2156404910, ss2628504663, ss2633148417, ss2700828031, ss2927559498, ss3012181625, ss3021567698, ss3350800095, ss3627214665, ss3631146565, ss3638049422, ss3641876805, ss3651960426, ss3679428924, ss3740370532, ss3752305339, ss3787661058, ss3792700544, ss3797584691, ss3833912152, ss3840549085, ss3881481099, ss3930490100, ss3985678530, ss4017669186, ss5213176892, ss5315735406, ss5415187634, ss5656197323, ss5841090177, ss5947624206, ss5980826145	NC_000014.8:50518825:C:A	NC_000014.9:50052107:C:A	(self)
83971251, 450828216, 1141816, 31279842, 1009301, 99800025, 185770166, 10102440853, ss2201879075, ss3027839992, ss3650204604, ss3696653272, ss3725446567, ss3771787832, ss3817639977, ss3846037922, ss3974901841, ss4970224507, ss5296179724, ss5490227405, ss5596445316, ss5765962921, ss5814740730, ss5851026534, ss5901288037	NC_000014.9:50052107:C:A	NC_000014.9:50052107:C:A	(self)
ss21204271	NT_026437.10:30438863:C:A	NC_000014.9:50052107:C:A	(self)
ss43579504, ss69156677, ss75078421, ss96916711, ss103184638, ss119815676, ss132323211, ss172268317	NT_026437.12:31518825:C:A	NC_000014.9:50052107:C:A	(self)
37667494, ss3930490100	NC_000014.8:50518825:C:G	NC_000014.9:50052107:C:G	(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 rs12891892

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

rs12891892