Name: rs12132517
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.

rs12132517

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:863421 (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: G>A / G>T
Variation Type: SNV Single Nucleotide Variation
Frequency: A=0.069485 (9647/138836, GnomAD)
A=0.09618 (1612/16760, 8.3KJPN)
A=0.02428 (369/15200, ALFA) (+ 12 more)
A=0.0735 (471/6404, 1000G_30x)
A=0.0741 (371/5008, 1000G)
A=0.0794 (306/3854, ALSPAC)
A=0.0871 (323/3708, TWINSUK)
A=0.1112 (325/2922, KOREAN)
A=0.1041 (117/1124, Daghestan)
A=0.087 (87/998, GoNL)
A=0.058 (35/600, NorthernSweden)
A=0.092 (22/240, HapMap)
A=0.102 (22/216, Qatari)
G=0.48 (32/66, SGDP_PRJ)
A=0.10 (4/40, 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	15200	G=0.97572	A=0.02428, T=0.00000
European	Sub	11108	G=0.96993	A=0.03007, T=0.00000
African	Sub	2624	G=0.9909	A=0.0091, T=0.0000
African Others	Sub	102	G=1.000	A=0.000, T=0.000
African American	Sub	2522	G=0.9905	A=0.0095, T=0.0000
Asian	Sub	98	G=1.00	A=0.00, T=0.00
East Asian	Sub	78	G=1.00	A=0.00, T=0.00
Other Asian	Sub	20	G=1.00	A=0.00, T=0.00
Latin American 1	Sub	130	G=1.000	A=0.000, T=0.000
Latin American 2	Sub	556	G=1.000	A=0.000, T=0.000
South Asian	Sub	78	G=1.00	A=0.00, T=0.00
Other	Sub	606	G=0.982	A=0.018, T=0.000

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
gnomAD - Genomes	Global	Study-wide	138836	G=0.930515	A=0.069485
gnomAD - Genomes	European	Sub	75658	G=0.91785	A=0.08215
gnomAD - Genomes	African	Sub	41270	G=0.95173	A=0.04827
gnomAD - Genomes	American	Sub	13550	G=0.94568	A=0.05432
gnomAD - Genomes	Ashkenazi Jewish	Sub	3278	G=0.9152	A=0.0848
gnomAD - Genomes	East Asian	Sub	2940	G=0.9109	A=0.0891
gnomAD - Genomes	Other	Sub	2140	G=0.9234	A=0.0766
8.3KJPN	JAPANESE	Study-wide	16760	G=0.90382	A=0.09618
Allele Frequency Aggregator	Total	Global	15200	G=0.97572	A=0.02428, T=0.00000
Allele Frequency Aggregator	European	Sub	11108	G=0.96993	A=0.03007, T=0.00000
Allele Frequency Aggregator	African	Sub	2624	G=0.9909	A=0.0091, T=0.0000
Allele Frequency Aggregator	Other	Sub	606	G=0.982	A=0.018, T=0.000
Allele Frequency Aggregator	Latin American 2	Sub	556	G=1.000	A=0.000, T=0.000
Allele Frequency Aggregator	Latin American 1	Sub	130	G=1.000	A=0.000, T=0.000
Allele Frequency Aggregator	Asian	Sub	98	G=1.00	A=0.00, T=0.00
Allele Frequency Aggregator	South Asian	Sub	78	G=1.00	A=0.00, T=0.00
1000Genomes_30x	Global	Study-wide	6404	G=0.9265	A=0.0735
1000Genomes_30x	African	Sub	1786	G=0.9317	A=0.0683
1000Genomes_30x	Europe	Sub	1266	G=0.9250	A=0.0750
1000Genomes_30x	South Asian	Sub	1202	G=0.9035	A=0.0965
1000Genomes_30x	East Asian	Sub	1170	G=0.9085	A=0.0915
1000Genomes_30x	American	Sub	980	G=0.968	A=0.032
1000Genomes	Global	Study-wide	5008	G=0.9259	A=0.0741
1000Genomes	African	Sub	1322	G=0.9395	A=0.0605
1000Genomes	East Asian	Sub	1008	G=0.9028	A=0.0972
1000Genomes	Europe	Sub	1006	G=0.9235	A=0.0765
1000Genomes	South Asian	Sub	978	G=0.903	A=0.097
1000Genomes	American	Sub	694	G=0.970	A=0.030
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.9206	A=0.0794
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.9129	A=0.0871
KOREAN population from KRGDB	KOREAN	Study-wide	2922	G=0.8888	A=0.1112
Genome-wide autozygosity in Daghestan	Global	Study-wide	1124	G=0.8959	A=0.1041
Genome-wide autozygosity in Daghestan	Daghestan	Sub	624	G=0.920	A=0.080
Genome-wide autozygosity in Daghestan	Near_East	Sub	142	G=0.880	A=0.120
Genome-wide autozygosity in Daghestan	Central Asia	Sub	122	G=0.811	A=0.189
Genome-wide autozygosity in Daghestan	Europe	Sub	108	G=0.907	A=0.093
Genome-wide autozygosity in Daghestan	South Asian	Sub	92	G=0.85	A=0.15
Genome-wide autozygosity in Daghestan	Caucasus	Sub	36	G=0.92	A=0.08
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	G=0.913	A=0.087
Northern Sweden	ACPOP	Study-wide	600	G=0.942	A=0.058
HapMap	Global	Study-wide	240	G=0.908	A=0.092
HapMap	African	Sub	120	G=0.925	A=0.075
HapMap	American	Sub	120	G=0.892	A=0.108
Qatari	Global	Study-wide	216	G=0.898	A=0.102
SGDP_PRJ	Global	Study-wide	66	G=0.48	A=0.52
The Danish reference pan genome	Danish	Study-wide	40	G=0.90	A=0.10

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.863421G>A
GRCh38.p14 chr 1	NC_000001.11:g.863421G>T
GRCh37.p13 chr 1	NC_000001.10:g.798801G>A
GRCh37.p13 chr 1	NC_000001.10:g.798801G>T

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	G=	A	T
GRCh38.p14 chr 1	NC_000001.11:g.863421=	NC_000001.11:g.863421G>A	NC_000001.11:g.863421G>T
GRCh37.p13 chr 1	NC_000001.10:g.798801=	NC_000001.10:g.798801G>A	NC_000001.10:g.798801G>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#.

40 SubSNP, 19 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_SNP	ss18273050	Feb 28, 2004 (120)
2	SSAHASNP	ss35170418	May 24, 2005 (125)
3	PERLEGEN	ss68756306	May 17, 2007 (127)
4	1000GENOMES	ss328358003	May 09, 2011 (134)
5	SSMP	ss647516441	Apr 25, 2013 (138)
6	EVA-GONL	ss974769607	Aug 21, 2014 (142)
7	1000GENOMES	ss1289340253	Aug 21, 2014 (142)
8	HAMMER_LAB	ss1397238519	Sep 08, 2015 (146)
9	DDI	ss1425684943	Apr 01, 2015 (144)
10	EVA_GENOME_DK	ss1573851215	Apr 01, 2015 (144)
11	EVA_DECODE	ss1584129638	Apr 01, 2015 (144)
12	EVA_UK10K_ALSPAC	ss1599378554	Apr 01, 2015 (144)
13	EVA_UK10K_TWINSUK	ss1642372587	Apr 01, 2015 (144)
14	WEILL_CORNELL_DGM	ss1917960780	Feb 12, 2016 (147)
15	JJLAB	ss2019498493	Sep 14, 2016 (149)
16	GRF	ss2697374858	Nov 08, 2017 (151)
17	GNOMAD	ss2750641660	Nov 08, 2017 (151)
18	SWEGEN	ss2986149482	Nov 08, 2017 (151)
19	CSHL	ss3343272690	Nov 08, 2017 (151)
20	EVA_DECODE	ss3685992500	Jul 12, 2019 (153)
21	ACPOP	ss3726716522	Jul 12, 2019 (153)
22	EVA	ss3745721198	Jul 12, 2019 (153)
23	KHV_HUMAN_GENOMES	ss3798743870	Jul 12, 2019 (153)
24	SGDP_PRJ	ss3847996154	Apr 25, 2020 (154)
25	KRGDB	ss3892836405	Apr 25, 2020 (154)
26	TOPMED	ss4436440139	Apr 25, 2021 (155)
27	TOPMED	ss4436440140	Apr 25, 2021 (155)
28	TOMMO_GENOMICS	ss5142053341	Apr 25, 2021 (155)
29	1000G_HIGH_COVERAGE	ss5240864338	Oct 12, 2022 (156)
30	EVA	ss5316184645	Oct 12, 2022 (156)
31	HUGCELL_USP	ss5442112643	Oct 12, 2022 (156)
32	1000G_HIGH_COVERAGE	ss5512489343	Oct 12, 2022 (156)
33	SANFORD_IMAGENETICS	ss5624749964	Oct 12, 2022 (156)
34	TOMMO_GENOMICS	ss5666192943	Oct 12, 2022 (156)
35	TOMMO_GENOMICS	ss5666192944	Oct 12, 2022 (156)
36	YY_MCH	ss5800244001	Oct 12, 2022 (156)
37	EVA	ss5831418723	Oct 12, 2022 (156)
38	EVA	ss5848748910	Oct 12, 2022 (156)
39	EVA	ss5906705275	Oct 12, 2022 (156)
40	EVA	ss5936583052	Oct 12, 2022 (156)
41	1000Genomes	NC_000001.10 - 798801	Oct 11, 2018 (152)
42	1000Genomes_30x	NC_000001.11 - 863421	Oct 12, 2022 (156)
43	The Avon Longitudinal Study of Parents and Children	NC_000001.10 - 798801	Oct 11, 2018 (152)
44	Genome-wide autozygosity in Daghestan	NC_000001.9 - 788664	Apr 25, 2020 (154)
45	The Danish reference pan genome	NC_000001.10 - 798801	Apr 25, 2020 (154)
46	gnomAD - Genomes	NC_000001.11 - 863421	Apr 25, 2021 (155)
47	Genome of the Netherlands Release 5	NC_000001.10 - 798801	Apr 25, 2020 (154)
48	HapMap	NC_000001.11 - 863421	Apr 25, 2020 (154)
49	KOREAN population from KRGDB	NC_000001.10 - 798801	Apr 25, 2020 (154)
50	Northern Sweden	NC_000001.10 - 798801	Jul 12, 2019 (153)
51	Qatari	NC_000001.10 - 798801	Apr 25, 2020 (154)
52	SGDP_PRJ	NC_000001.10 - 798801	Apr 25, 2020 (154)
53	8.3KJPN	NC_000001.10 - 798801	Apr 25, 2021 (155)
54	14KJPN Submission ignored due to conflicting rows: Row 30047 (NC_000001.11:863420:G:A 2257/28258) Row 30048 (NC_000001.11:863420:G:T 1/28258)	-	Oct 12, 2022 (156)
55	14KJPN Submission ignored due to conflicting rows: Row 30047 (NC_000001.11:863420:G:A 2257/28258) Row 30048 (NC_000001.11:863420:G:T 1/28258)	-	Oct 12, 2022 (156)
56	TopMed Submission ignored due to conflicting rows: Row 46474 (NC_000001.11:863420:G:A 17872/264690) Row 46475 (NC_000001.11:863420:G:T 1/264690)	-	Apr 25, 2021 (155)
57	TopMed Submission ignored due to conflicting rows: Row 46474 (NC_000001.11:863420:G:A 17872/264690) Row 46475 (NC_000001.11:863420:G:T 1/264690)	-	Apr 25, 2021 (155)
58	UK 10K study - Twins	NC_000001.10 - 798801	Oct 11, 2018 (152)
59	ALFA	NC_000001.11 - 863421	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
ss35170418	NC_000001.8:838663:G:A	NC_000001.11:863420:G:A	(self)
6, ss1397238519, ss1584129638	NC_000001.9:788663:G:A	NC_000001.11:863420:G:A	(self)
5020, 518, 1358449, 634, 13799, 1387, 2710, 13134, 22648, 518, ss328358003, ss647516441, ss974769607, ss1289340253, ss1425684943, ss1573851215, ss1599378554, ss1642372587, ss1917960780, ss2019498493, ss2697374858, ss2750641660, ss2986149482, ss3343272690, ss3726716522, ss3745721198, ss3847996154, ss3892836405, ss5142053341, ss5316184645, ss5624749964, ss5831418723, ss5936583052	NC_000001.10:798800:G:A	NC_000001.11:863420:G:A	(self)
15278, 71334, 83, 942023499, ss3685992500, ss3798743870, ss4436440139, ss5240864338, ss5442112643, ss5512489343, ss5666192943, ss5800244001, ss5848748910, ss5906705275	NC_000001.11:863420:G:A	NC_000001.11:863420:G:A	(self)
ss68756306	NT_004350.19:277432:G:A	NC_000001.11:863420:G:A	(self)
ss18273050	NT_034471.3:277432:G:A	NC_000001.11:863420:G:A	(self)
942023499, ss4436440140, ss5666192944	NC_000001.11:863420:G:T	NC_000001.11:863420:G: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 rs12132517

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

rs12132517