Name: rs12512084
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.

rs12512084

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr4:99252002 (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>G
Variation Type: SNV Single Nucleotide Variation
Frequency: G=0.372133 (98500/264690, TOPMED)
G=0.379787 (53158/139968, GnomAD)
G=0.09665 (2731/28258, 14KJPN) (+ 14 more)
G=0.41271 (7796/18890, ALFA)
G=0.09302 (1559/16760, 8.3KJPN)
G=0.2798 (1792/6404, 1000G_30x)
G=0.2740 (1372/5008, 1000G)
G=0.4435 (1987/4480, Estonian)
G=0.4642 (1789/3854, ALSPAC)
G=0.4798 (1779/3708, TWINSUK)
G=0.1394 (407/2920, KOREAN)
G=0.426 (425/998, GoNL)
G=0.487 (292/600, NorthernSweden)
A=0.389 (115/296, SGDP_PRJ)
G=0.361 (78/216, Qatari)
A=0.29 (12/42, Siberian)
G=0.38 (15/40, GENOME_DK)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: LOC100507053 : 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: 20231103111315

Population	Group	Sample Size	Ref Allele	Alt Allele	Ref HMOZ	Alt HMOZ	HTRZ	HWEP
Total	Global	18890	A=0.58729	G=0.41271	0.350768	0.176178	0.473055	3
European	Sub	14286	A=0.53738	G=0.46262	0.280554	0.205796	0.51365	5
African	Sub	2946	A=0.8306	G=0.1694	0.684997	0.023761	0.291242	1
African Others	Sub	114	A=0.877	G=0.123	0.789474	0.035088	0.175439	1
African American	Sub	2832	A=0.8287	G=0.1713	0.680791	0.023305	0.295904	2
Asian	Sub	112	A=0.929	G=0.071	0.857143	0.0	0.142857	0
East Asian	Sub	86	A=0.93	G=0.07	0.860465	0.0	0.139535	0
Other Asian	Sub	26	A=0.92	G=0.08	0.846154	0.0	0.153846	0
Latin American 1	Sub	146	A=0.521	G=0.479	0.30137	0.260274	0.438356	1
Latin American 2	Sub	610	A=0.493	G=0.507	0.239344	0.252459	0.508197	0
South Asian	Sub	98	A=0.83	G=0.17	0.714286	0.061224	0.22449	2
Other	Sub	692	A=0.590	G=0.410	0.352601	0.17341	0.473988	0

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=0.627867	G=0.372133
gnomAD - Genomes	Global	Study-wide	139968	A=0.620213	G=0.379787
gnomAD - Genomes	European	Sub	75814	A=0.53196	G=0.46804
gnomAD - Genomes	African	Sub	41952	A=0.81555	G=0.18445
gnomAD - Genomes	American	Sub	13606	A=0.49728	G=0.50272
gnomAD - Genomes	Ashkenazi Jewish	Sub	3320	A=0.4518	G=0.5482
gnomAD - Genomes	East Asian	Sub	3128	A=0.8737	G=0.1263
gnomAD - Genomes	Other	Sub	2148	A=0.5899	G=0.4101
14KJPN	JAPANESE	Study-wide	28258	A=0.90335	G=0.09665
Allele Frequency Aggregator	Total	Global	18890	A=0.58729	G=0.41271
Allele Frequency Aggregator	European	Sub	14286	A=0.53738	G=0.46262
Allele Frequency Aggregator	African	Sub	2946	A=0.8306	G=0.1694
Allele Frequency Aggregator	Other	Sub	692	A=0.590	G=0.410
Allele Frequency Aggregator	Latin American 2	Sub	610	A=0.493	G=0.507
Allele Frequency Aggregator	Latin American 1	Sub	146	A=0.521	G=0.479
Allele Frequency Aggregator	Asian	Sub	112	A=0.929	G=0.071
Allele Frequency Aggregator	South Asian	Sub	98	A=0.83	G=0.17
8.3KJPN	JAPANESE	Study-wide	16760	A=0.90698	G=0.09302
1000Genomes_30x	Global	Study-wide	6404	A=0.7202	G=0.2798
1000Genomes_30x	African	Sub	1786	A=0.8617	G=0.1383
1000Genomes_30x	Europe	Sub	1266	A=0.5039	G=0.4961
1000Genomes_30x	South Asian	Sub	1202	A=0.8270	G=0.1730
1000Genomes_30x	East Asian	Sub	1170	A=0.8667	G=0.1333
1000Genomes_30x	American	Sub	980	A=0.436	G=0.564
1000Genomes	Global	Study-wide	5008	A=0.7260	G=0.2740
1000Genomes	African	Sub	1322	A=0.8533	G=0.1467
1000Genomes	East Asian	Sub	1008	A=0.8750	G=0.1250
1000Genomes	Europe	Sub	1006	A=0.5060	G=0.4940
1000Genomes	South Asian	Sub	978	A=0.830	G=0.170
1000Genomes	American	Sub	694	A=0.439	G=0.561
Genetic variation in the Estonian population	Estonian	Study-wide	4480	A=0.5565	G=0.4435
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.5358	G=0.4642
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.5202	G=0.4798
KOREAN population from KRGDB	KOREAN	Study-wide	2920	A=0.8606	G=0.1394
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	A=0.574	G=0.426
Northern Sweden	ACPOP	Study-wide	600	A=0.513	G=0.487
SGDP_PRJ	Global	Study-wide	296	A=0.389	G=0.611
Qatari	Global	Study-wide	216	A=0.639	G=0.361
Siberian	Global	Study-wide	42	A=0.29	G=0.71
The Danish reference pan genome	Danish	Study-wide	40	A=0.62	G=0.38

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 4	NC_000004.12:g.99252002A>G
GRCh37.p13 chr 4	NC_000004.11:g.100173159A>G

Gene: LOC100507053, uncharacterized LOC100507053 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC100507053 transcript	NR_037884.1: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	A=	G
GRCh38.p14 chr 4	NC_000004.12:g.99252002=	NC_000004.12:g.99252002A>G
GRCh37.p13 chr 4	NC_000004.11:g.100173159=	NC_000004.11:g.100173159A>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#.

63 SubSNP, 17 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	CSHL-HAPMAP	ss19603273	Feb 28, 2004 (120)
2	ABI	ss42165067	Mar 14, 2006 (126)
3	HGSV	ss80751081	Dec 16, 2007 (130)
4	HUMANGENOME_JCVI	ss98986802	Feb 06, 2009 (130)
5	1000GENOMES	ss108170939	Jan 23, 2009 (130)
6	ILLUMINA-UK	ss117113674	Feb 14, 2009 (130)
7	COMPLETE_GENOMICS	ss162380159	Jul 04, 2010 (132)
8	1000GENOMES	ss221098756	Jul 14, 2010 (132)
9	1000GENOMES	ss232515108	Jul 14, 2010 (132)
10	1000GENOMES	ss239780120	Jul 15, 2010 (132)
11	BL	ss253372088	May 09, 2011 (134)
12	GMI	ss277844401	May 04, 2012 (137)
13	PJP	ss293147503	May 09, 2011 (134)
14	TISHKOFF	ss557721159	Apr 25, 2013 (138)
15	SSMP	ss651525717	Apr 25, 2013 (138)
16	EVA-GONL	ss980450167	Aug 21, 2014 (142)
17	JMKIDD_LAB	ss1071787157	Aug 21, 2014 (142)
18	1000GENOMES	ss1310980089	Aug 21, 2014 (142)
19	DDI	ss1429982726	Apr 01, 2015 (144)
20	EVA_GENOME_DK	ss1580687449	Apr 01, 2015 (144)
21	EVA_DECODE	ss1589954193	Apr 01, 2015 (144)
22	EVA_UK10K_ALSPAC	ss1610736390	Apr 01, 2015 (144)
23	EVA_UK10K_TWINSUK	ss1653730423	Apr 01, 2015 (144)
24	HAMMER_LAB	ss1801909793	Sep 08, 2015 (146)
25	WEILL_CORNELL_DGM	ss1923690231	Feb 12, 2016 (147)
26	GENOMED	ss1969816833	Jul 19, 2016 (147)
27	JJLAB	ss2022431064	Sep 14, 2016 (149)
28	USC_VALOUEV	ss2150560241	Dec 20, 2016 (150)
29	HUMAN_LONGEVITY	ss2265425730	Dec 20, 2016 (150)
30	GRF	ss2706037113	Nov 08, 2017 (151)
31	GNOMAD	ss2812855201	Nov 08, 2017 (151)
32	SWEGEN	ss2995210582	Nov 08, 2017 (151)
33	BIOINF_KMB_FNS_UNIBA	ss3024990800	Nov 08, 2017 (151)
34	CSHL	ss3345861829	Nov 08, 2017 (151)
35	URBANLAB	ss3647802643	Oct 12, 2018 (152)
36	EGCUT_WGS	ss3663106401	Jul 13, 2019 (153)
37	EVA_DECODE	ss3712656944	Jul 13, 2019 (153)
38	ACPOP	ss3731421844	Jul 13, 2019 (153)
39	EVA	ss3762167145	Jul 13, 2019 (153)
40	PACBIO	ss3784801972	Jul 13, 2019 (153)
41	PACBIO	ss3790246631	Jul 13, 2019 (153)
42	PACBIO	ss3795122035	Jul 13, 2019 (153)
43	KHV_HUMAN_GENOMES	ss3805315566	Jul 13, 2019 (153)
44	EVA	ss3828703566	Apr 26, 2020 (154)
45	EVA	ss3837792863	Apr 26, 2020 (154)
46	EVA	ss3843231256	Apr 26, 2020 (154)
47	SGDP_PRJ	ss3859610747	Apr 26, 2020 (154)
48	KRGDB	ss3905888275	Apr 26, 2020 (154)
49	TOPMED	ss4624642741	Apr 26, 2021 (155)
50	TOMMO_GENOMICS	ss5167078796	Apr 26, 2021 (155)
51	1000G_HIGH_COVERAGE	ss5260288746	Oct 13, 2022 (156)
52	EVA	ss5350976747	Oct 13, 2022 (156)
53	HUGCELL_USP	ss5458931154	Oct 13, 2022 (156)
54	EVA	ss5507641505	Oct 13, 2022 (156)
55	1000G_HIGH_COVERAGE	ss5541956759	Oct 13, 2022 (156)
56	SANFORD_IMAGENETICS	ss5635665736	Oct 13, 2022 (156)
57	TOMMO_GENOMICS	ss5701810115	Oct 13, 2022 (156)
58	YY_MCH	ss5805354053	Oct 13, 2022 (156)
59	EVA	ss5844424300	Oct 13, 2022 (156)
60	EVA	ss5854356002	Oct 13, 2022 (156)
61	EVA	ss5864677350	Oct 13, 2022 (156)
62	EVA	ss5964056431	Oct 13, 2022 (156)
63	EVA	ss5980240207	Oct 13, 2022 (156)
64	1000Genomes	NC_000004.11 - 100173159	Oct 12, 2018 (152)
65	1000Genomes_30x	NC_000004.12 - 99252002	Oct 13, 2022 (156)
66	The Avon Longitudinal Study of Parents and Children	NC_000004.11 - 100173159	Oct 12, 2018 (152)
67	Genetic variation in the Estonian population	NC_000004.11 - 100173159	Oct 12, 2018 (152)
68	The Danish reference pan genome	NC_000004.11 - 100173159	Apr 26, 2020 (154)
69	gnomAD - Genomes	NC_000004.12 - 99252002	Apr 26, 2021 (155)
70	Genome of the Netherlands Release 5	NC_000004.11 - 100173159	Apr 26, 2020 (154)
71	KOREAN population from KRGDB	NC_000004.11 - 100173159	Apr 26, 2020 (154)
72	Northern Sweden	NC_000004.11 - 100173159	Jul 13, 2019 (153)
73	Qatari	NC_000004.11 - 100173159	Apr 26, 2020 (154)
74	SGDP_PRJ	NC_000004.11 - 100173159	Apr 26, 2020 (154)
75	Siberian	NC_000004.11 - 100173159	Apr 26, 2020 (154)
76	8.3KJPN	NC_000004.11 - 100173159	Apr 26, 2021 (155)
77	14KJPN	NC_000004.12 - 99252002	Oct 13, 2022 (156)
78	TopMed	NC_000004.12 - 99252002	Apr 26, 2021 (155)
79	UK 10K study - Twins	NC_000004.11 - 100173159	Oct 12, 2018 (152)
80	ALFA	NC_000004.12 - 99252002	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).

Associated ID	History Updated (Build)
rs61123557	May 26, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss80751081	NC_000004.9:100530336:A:G	NC_000004.12:99252001:A:G	(self)
ss108170939, ss117113674, ss162380159, ss253372088, ss277844401, ss293147503, ss1589954193	NC_000004.10:100392181:A:G	NC_000004.12:99252001:A:G	(self)
22422294, 12472612, 8844649, 6852388, 5513649, 13065669, 4706709, 5732161, 11627727, 3076595, 25048103, 12472612, ss221098756, ss232515108, ss239780120, ss557721159, ss651525717, ss980450167, ss1071787157, ss1310980089, ss1429982726, ss1580687449, ss1610736390, ss1653730423, ss1801909793, ss1923690231, ss1969816833, ss2022431064, ss2150560241, ss2706037113, ss2812855201, ss2995210582, ss3345861829, ss3663106401, ss3731421844, ss3762167145, ss3784801972, ss3790246631, ss3795122035, ss3828703566, ss3837792863, ss3859610747, ss3905888275, ss5167078796, ss5350976747, ss5507641505, ss5635665736, ss5844424300, ss5964056431, ss5980240207	NC_000004.11:100173158:A:G	NC_000004.12:99252001:A:G	(self)
29482694, 158835725, 35647219, 462020297, 6492382410, ss2265425730, ss3024990800, ss3647802643, ss3712656944, ss3805315566, ss3843231256, ss4624642741, ss5260288746, ss5458931154, ss5541956759, ss5701810115, ss5805354053, ss5854356002, ss5864677350	NC_000004.12:99252001:A:G	NC_000004.12:99252001:A:G	(self)
ss19603273	NT_016354.16:24667862:A:G	NC_000004.12:99252001:A:G	(self)
ss42165067, ss98986802	NT_016354.19:24720879:A:G	NC_000004.12:99252001:A: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 rs12512084

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

rs12512084