Name: rs12116433
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.

rs12116433

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:159613693 (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=0.017598 (4658/264690, TOPMED)
T=0.017130 (2403/140282, GnomAD)
T=0.02165 (409/18890, ALFA) (+ 10 more)
T=0.0105 (67/6404, 1000G_30x)
T=0.0116 (58/5008, 1000G)
T=0.0214 (96/4480, Estonian)
T=0.0335 (129/3854, ALSPAC)
T=0.0326 (121/3708, TWINSUK)
T=0.035 (35/998, GoNL)
T=0.057 (34/600, NorthernSweden)
T=0.03 (1/40, GENOME_DK)
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	18890	C=0.97835	T=0.02165
European	Sub	14286	C=0.97389	T=0.02611
African	Sub	2946	C=0.9969	T=0.0031
African Others	Sub	114	C=1.000	T=0.000
African American	Sub	2832	C=0.9968	T=0.0032
Asian	Sub	112	C=1.000	T=0.000
East Asian	Sub	86	C=1.00	T=0.00
Other Asian	Sub	26	C=1.00	T=0.00
Latin American 1	Sub	146	C=0.979	T=0.021
Latin American 2	Sub	610	C=0.984	T=0.016
South Asian	Sub	98	C=0.98	T=0.02
Other	Sub	692	C=0.983	T=0.017

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=0.982402	T=0.017598
gnomAD - Genomes	Global	Study-wide	140282	C=0.982870	T=0.017130
gnomAD - Genomes	European	Sub	75948	C=0.97534	T=0.02466
gnomAD - Genomes	African	Sub	42064	C=0.99479	T=0.00521
gnomAD - Genomes	American	Sub	13660	C=0.98411	T=0.01589
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	C=0.9856	T=0.0144
gnomAD - Genomes	East Asian	Sub	3132	C=1.0000	T=0.0000
gnomAD - Genomes	Other	Sub	2154	C=0.9786	T=0.0214
Allele Frequency Aggregator	Total	Global	18890	C=0.97835	T=0.02165
Allele Frequency Aggregator	European	Sub	14286	C=0.97389	T=0.02611
Allele Frequency Aggregator	African	Sub	2946	C=0.9969	T=0.0031
Allele Frequency Aggregator	Other	Sub	692	C=0.983	T=0.017
Allele Frequency Aggregator	Latin American 2	Sub	610	C=0.984	T=0.016
Allele Frequency Aggregator	Latin American 1	Sub	146	C=0.979	T=0.021
Allele Frequency Aggregator	Asian	Sub	112	C=1.000	T=0.000
Allele Frequency Aggregator	South Asian	Sub	98	C=0.98	T=0.02
1000Genomes_30x	Global	Study-wide	6404	C=0.9895	T=0.0105
1000Genomes_30x	African	Sub	1786	C=0.9989	T=0.0011
1000Genomes_30x	Europe	Sub	1266	C=0.9763	T=0.0237
1000Genomes_30x	South Asian	Sub	1202	C=0.9784	T=0.0216
1000Genomes_30x	East Asian	Sub	1170	C=1.0000	T=0.0000
1000Genomes_30x	American	Sub	980	C=0.991	T=0.009
1000Genomes	Global	Study-wide	5008	C=0.9884	T=0.0116
1000Genomes	African	Sub	1322	C=0.9992	T=0.0008
1000Genomes	East Asian	Sub	1008	C=1.0000	T=0.0000
1000Genomes	Europe	Sub	1006	C=0.9761	T=0.0239
1000Genomes	South Asian	Sub	978	C=0.975	T=0.025
1000Genomes	American	Sub	694	C=0.987	T=0.013
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.9786	T=0.0214
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.9665	T=0.0335
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.9674	T=0.0326
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.965	T=0.035
Northern Sweden	ACPOP	Study-wide	600	C=0.943	T=0.057
The Danish reference pan genome	Danish	Study-wide	40	C=0.97	T=0.03
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.159613693C>T
GRCh37.p13 chr 1	NC_000001.10:g.159583483C>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.159613693=	NC_000001.11:g.159613693C>T
GRCh37.p13 chr 1	NC_000001.10:g.159583483=	NC_000001.10:g.159583483C>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#.

34 SubSNP, 12 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_SNP	ss18243021	Feb 28, 2004 (120)
2	1000GENOMES	ss230744590	Jul 14, 2010 (132)
3	ILLUMINA	ss536096770	Sep 08, 2015 (146)
4	EVA-GONL	ss975718741	Aug 21, 2014 (142)
5	1000GENOMES	ss1293065786	Aug 21, 2014 (142)
6	EVA_GENOME_DK	ss1574414846	Apr 01, 2015 (144)
7	EVA_DECODE	ss1585101828	Apr 01, 2015 (144)
8	EVA_UK10K_ALSPAC	ss1601287626	Apr 01, 2015 (144)
9	EVA_UK10K_TWINSUK	ss1644281659	Apr 01, 2015 (144)
10	JJLAB	ss2019991503	Sep 14, 2016 (149)
11	HUMAN_LONGEVITY	ss2166823627	Dec 20, 2016 (150)
12	GNOMAD	ss2761721484	Nov 08, 2017 (151)
13	SWEGEN	ss2987809710	Nov 08, 2017 (151)
14	CSHL	ss3343726163	Nov 08, 2017 (151)
15	ILLUMINA	ss3626217948	Oct 11, 2018 (152)
16	EGCUT_WGS	ss3655751086	Jul 12, 2019 (153)
17	EVA_DECODE	ss3687851676	Jul 12, 2019 (153)
18	ACPOP	ss3727514992	Jul 12, 2019 (153)
19	KHV_HUMAN_GENOMES	ss3799851052	Jul 12, 2019 (153)
20	EVA	ss3826442920	Apr 25, 2020 (154)
21	SGDP_PRJ	ss3850077303	Apr 25, 2020 (154)
22	TOPMED	ss4469561511	Apr 25, 2021 (155)
23	1000G_HIGH_COVERAGE	ss5244414303	Oct 12, 2022 (156)
24	EVA	ss5322271823	Oct 12, 2022 (156)
25	HUGCELL_USP	ss5444991447	Oct 12, 2022 (156)
26	EVA	ss5506042051	Oct 12, 2022 (156)
27	1000G_HIGH_COVERAGE	ss5517803681	Oct 12, 2022 (156)
28	SANFORD_IMAGENETICS	ss5624219033	Oct 12, 2022 (156)
29	SANFORD_IMAGENETICS	ss5626659466	Oct 12, 2022 (156)
30	EVA	ss5832713270	Oct 12, 2022 (156)
31	EVA	ss5847559000	Oct 12, 2022 (156)
32	EVA	ss5910383554	Oct 12, 2022 (156)
33	EVA	ss5938456042	Oct 12, 2022 (156)
34	EVA	ss5979291587	Oct 12, 2022 (156)
35	1000Genomes	NC_000001.10 - 159583483	Oct 11, 2018 (152)
36	1000Genomes_30x	NC_000001.11 - 159613693	Oct 12, 2022 (156)
37	The Avon Longitudinal Study of Parents and Children	NC_000001.10 - 159583483	Oct 11, 2018 (152)
38	Genetic variation in the Estonian population	NC_000001.10 - 159583483	Oct 11, 2018 (152)
39	The Danish reference pan genome	NC_000001.10 - 159583483	Apr 25, 2020 (154)
40	gnomAD - Genomes	NC_000001.11 - 159613693	Apr 25, 2021 (155)
41	Genome of the Netherlands Release 5	NC_000001.10 - 159583483	Apr 25, 2020 (154)
42	Northern Sweden	NC_000001.10 - 159583483	Jul 12, 2019 (153)
43	SGDP_PRJ	NC_000001.10 - 159583483	Apr 25, 2020 (154)
44	TopMed	NC_000001.11 - 159613693	Apr 25, 2021 (155)
45	UK 10K study - Twins	NC_000001.10 - 159583483	Oct 11, 2018 (152)
46	ALFA	NC_000001.11 - 159613693	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
ss1585101828	NC_000001.9:157850106:C:T	NC_000001.11:159613692:C:T	(self)
3862336, 2101878, 1489334, 1721717, 912906, 799857, 2094283, 2101878, ss230744590, ss536096770, ss975718741, ss1293065786, ss1574414846, ss1601287626, ss1644281659, ss2019991503, ss2761721484, ss2987809710, ss3343726163, ss3626217948, ss3655751086, ss3727514992, ss3826442920, ss3850077303, ss5322271823, ss5506042051, ss5624219033, ss5626659466, ss5832713270, ss5847559000, ss5938456042, ss5979291587	NC_000001.10:159583482:C:T	NC_000001.11:159613692:C:T	(self)
5329616, 28085903, 33167846, 1666929178, ss2166823627, ss3687851676, ss3799851052, ss4469561511, ss5244414303, ss5444991447, ss5517803681, ss5910383554	NC_000001.11:159613692:C:T	NC_000001.11:159613692:C:T	(self)
ss18243021	NT_079484.1:6033314:C:T	NC_000001.11:159613692: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 rs12116433

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.

Choose placement

dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs12116433