Name: rs12025677
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.

rs12025677

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:67894204 (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: T>C
Variation Type: SNV Single Nucleotide Variation
Frequency: C=0.337002 (89201/264690, TOPMED)
C=0.327477 (45837/139970, GnomAD)
C=0.33357 (9426/28258, 14KJPN) (+ 17 more)
C=0.30139 (7745/25698, ALFA)
C=0.33705 (5649/16760, 8.3KJPN)
C=0.3240 (2075/6404, 1000G_30x)
C=0.3291 (1648/5008, 1000G)
C=0.2167 (971/4480, Estonian)
C=0.3010 (1160/3854, ALSPAC)
C=0.3112 (1154/3708, TWINSUK)
C=0.3454 (1012/2930, KOREAN)
C=0.3790 (717/1892, HapMap)
C=0.260 (259/998, GoNL)
C=0.283 (177/626, Chileans)
C=0.260 (156/600, NorthernSweden)
T=0.350 (96/274, SGDP_PRJ)
T=0.491 (106/216, Qatari)
C=0.405 (85/210, Vietnamese)
C=0.23 (9/40, GENOME_DK)
T=0.46 (11/24, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: GNG12-AS1 : 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	25698	T=0.69861	C=0.30139
European	Sub	17396	T=0.71137	C=0.28863
African	Sub	3624	T=0.6145	C=0.3855
African Others	Sub	126	T=0.492	C=0.508
African American	Sub	3498	T=0.6189	C=0.3811
Asian	Sub	160	T=0.769	C=0.231
East Asian	Sub	102	T=0.735	C=0.265
Other Asian	Sub	58	T=0.83	C=0.17
Latin American 1	Sub	292	T=0.668	C=0.332
Latin American 2	Sub	2770	T=0.7303	C=0.2697
South Asian	Sub	110	T=0.745	C=0.255
Other	Sub	1346	T=0.6895	C=0.3105

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	T=0.662998	C=0.337002
gnomAD - Genomes	Global	Study-wide	139970	T=0.672523	C=0.327477
gnomAD - Genomes	European	Sub	75844	T=0.71254	C=0.28746
gnomAD - Genomes	African	Sub	41910	T=0.60826	C=0.39174
gnomAD - Genomes	American	Sub	13628	T=0.69078	C=0.30922
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	T=0.5099	C=0.4901
gnomAD - Genomes	East Asian	Sub	3112	T=0.6587	C=0.3413
gnomAD - Genomes	Other	Sub	2152	T=0.6691	C=0.3309
14KJPN	JAPANESE	Study-wide	28258	T=0.66643	C=0.33357
Allele Frequency Aggregator	Total	Global	25698	T=0.69861	C=0.30139
Allele Frequency Aggregator	European	Sub	17396	T=0.71137	C=0.28863
Allele Frequency Aggregator	African	Sub	3624	T=0.6145	C=0.3855
Allele Frequency Aggregator	Latin American 2	Sub	2770	T=0.7303	C=0.2697
Allele Frequency Aggregator	Other	Sub	1346	T=0.6895	C=0.3105
Allele Frequency Aggregator	Latin American 1	Sub	292	T=0.668	C=0.332
Allele Frequency Aggregator	Asian	Sub	160	T=0.769	C=0.231
Allele Frequency Aggregator	South Asian	Sub	110	T=0.745	C=0.255
8.3KJPN	JAPANESE	Study-wide	16760	T=0.66295	C=0.33705
1000Genomes_30x	Global	Study-wide	6404	T=0.6760	C=0.3240
1000Genomes_30x	African	Sub	1786	T=0.5952	C=0.4048
1000Genomes_30x	Europe	Sub	1266	T=0.6856	C=0.3144
1000Genomes_30x	South Asian	Sub	1202	T=0.7903	C=0.2097
1000Genomes_30x	East Asian	Sub	1170	T=0.6444	C=0.3556
1000Genomes_30x	American	Sub	980	T=0.708	C=0.292
1000Genomes	Global	Study-wide	5008	T=0.6709	C=0.3291
1000Genomes	African	Sub	1322	T=0.5862	C=0.4138
1000Genomes	East Asian	Sub	1008	T=0.6399	C=0.3601
1000Genomes	Europe	Sub	1006	T=0.6819	C=0.3181
1000Genomes	South Asian	Sub	978	T=0.778	C=0.222
1000Genomes	American	Sub	694	T=0.710	C=0.290
Genetic variation in the Estonian population	Estonian	Study-wide	4480	T=0.7833	C=0.2167
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.6990	C=0.3010
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.6888	C=0.3112
KOREAN population from KRGDB	KOREAN	Study-wide	2930	T=0.6546	C=0.3454
HapMap	Global	Study-wide	1892	T=0.6210	C=0.3790
HapMap	American	Sub	770	T=0.740	C=0.260
HapMap	African	Sub	692	T=0.484	C=0.516
HapMap	Asian	Sub	254	T=0.638	C=0.362
HapMap	Europe	Sub	176	T=0.614	C=0.386
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.740	C=0.260
Chileans	Chilean	Study-wide	626	T=0.717	C=0.283
Northern Sweden	ACPOP	Study-wide	600	T=0.740	C=0.260
SGDP_PRJ	Global	Study-wide	274	T=0.350	C=0.650
Qatari	Global	Study-wide	216	T=0.491	C=0.509
A Vietnamese Genetic Variation Database	Global	Study-wide	210	T=0.595	C=0.405
The Danish reference pan genome	Danish	Study-wide	40	T=0.78	C=0.23
Siberian	Global	Study-wide	24	T=0.46	C=0.54

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.67894204T>C
GRCh37.p13 chr 1	NC_000001.10:g.68359887T>C

Gene: GNG12-AS1, GNG12, DIRAS3 and WLS antisense RNA 1 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
GNG12-AS1 transcript	NR_040077.1: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	T=	C
GRCh38.p14 chr 1	NC_000001.11:g.67894204=	NC_000001.11:g.67894204T>C
GRCh37.p13 chr 1	NC_000001.10:g.68359887=	NC_000001.10:g.68359887T>C

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#.

69 SubSNP, 20 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_SNP	ss18077628	Feb 28, 2004 (120)
2	PERLEGEN	ss23177273	Sep 20, 2004 (123)
3	ABI	ss43812514	Mar 14, 2006 (126)
4	AFFY	ss66040662	Nov 29, 2006 (127)
5	AFFY	ss75933606	Dec 06, 2007 (129)
6	KRIBB_YJKIM	ss82944826	Dec 15, 2007 (130)
7	BGI	ss106573356	Feb 06, 2009 (130)
8	1000GENOMES	ss110589529	Jan 25, 2009 (130)
9	ILLUMINA-UK	ss118773753	Feb 14, 2009 (130)
10	GMI	ss155129438	Dec 01, 2009 (131)
11	ENSEMBL	ss161269972	Dec 01, 2009 (131)
12	COMPLETE_GENOMICS	ss163480832	Jul 04, 2010 (132)
13	COMPLETE_GENOMICS	ss164481687	Jul 04, 2010 (132)
14	AFFY	ss169322178	Jul 04, 2010 (132)
15	BUSHMAN	ss198574950	Jul 04, 2010 (132)
16	BCM-HGSC-SUB	ss205094893	Jul 04, 2010 (132)
17	1000GENOMES	ss218434774	Jul 14, 2010 (132)
18	1000GENOMES	ss230571174	Jul 14, 2010 (132)
19	1000GENOMES	ss238258593	Jul 15, 2010 (132)
20	GMI	ss275862395	May 04, 2012 (137)
21	GMI	ss284066221	Apr 25, 2013 (138)
22	PJP	ss290530195	May 09, 2011 (134)
23	TISHKOFF	ss554213613	Apr 25, 2013 (138)
24	SSMP	ss648089992	Apr 25, 2013 (138)
25	EVA-GONL	ss975254193	Aug 21, 2014 (142)
26	JMKIDD_LAB	ss1067959392	Aug 21, 2014 (142)
27	1000GENOMES	ss1291249859	Aug 21, 2014 (142)
28	DDI	ss1425840012	Apr 01, 2015 (144)
29	EVA_GENOME_DK	ss1574124979	Apr 01, 2015 (144)
30	EVA_DECODE	ss1584624047	Apr 01, 2015 (144)
31	EVA_UK10K_ALSPAC	ss1600364561	Apr 01, 2015 (144)
32	EVA_UK10K_TWINSUK	ss1643358594	Apr 01, 2015 (144)
33	EVA_SVP	ss1712340851	Apr 01, 2015 (144)
34	HAMMER_LAB	ss1794506607	Sep 08, 2015 (146)
35	WEILL_CORNELL_DGM	ss1918461804	Feb 12, 2016 (147)
36	GENOMED	ss1966768346	Jul 19, 2016 (147)
37	JJLAB	ss2019748442	Sep 14, 2016 (149)
38	USC_VALOUEV	ss2147764472	Dec 20, 2016 (150)
39	HUMAN_LONGEVITY	ss2163249139	Dec 20, 2016 (150)
40	GRF	ss2697682450	Nov 08, 2017 (151)
41	GNOMAD	ss2756155898	Nov 08, 2017 (151)
42	SWEGEN	ss2986959564	Nov 08, 2017 (151)
43	BIOINF_KMB_FNS_UNIBA	ss3023636204	Nov 08, 2017 (151)
44	CSHL	ss3343496209	Nov 08, 2017 (151)
45	EGCUT_WGS	ss3655030378	Jul 12, 2019 (153)
46	EVA_DECODE	ss3686947631	Jul 12, 2019 (153)
47	ACPOP	ss3727125854	Jul 12, 2019 (153)
48	EVA	ss3746315038	Jul 12, 2019 (153)
49	PACBIO	ss3783435219	Jul 12, 2019 (153)
50	PACBIO	ss3789089576	Jul 12, 2019 (153)
51	PACBIO	ss3793962313	Jul 12, 2019 (153)
52	KHV_HUMAN_GENOMES	ss3799321542	Jul 12, 2019 (153)
53	EVA	ss3826218412	Apr 25, 2020 (154)
54	SGDP_PRJ	ss3849034203	Apr 25, 2020 (154)
55	KRGDB	ss3894063373	Apr 25, 2020 (154)
56	TOPMED	ss4452889401	Apr 25, 2021 (155)
57	TOMMO_GENOMICS	ss5144350482	Apr 25, 2021 (155)
58	1000G_HIGH_COVERAGE	ss5242579470	Oct 12, 2022 (156)
59	EVA	ss5319298408	Oct 12, 2022 (156)
60	HUGCELL_USP	ss5443611959	Oct 12, 2022 (156)
61	EVA	ss5505882587	Oct 12, 2022 (156)
62	1000G_HIGH_COVERAGE	ss5515011500	Oct 12, 2022 (156)
63	SANFORD_IMAGENETICS	ss5625706997	Oct 12, 2022 (156)
64	TOMMO_GENOMICS	ss5669237260	Oct 12, 2022 (156)
65	YY_MCH	ss5800674316	Oct 12, 2022 (156)
66	EVA	ss5832080282	Oct 12, 2022 (156)
67	EVA	ss5848944871	Oct 12, 2022 (156)
68	EVA	ss5908619366	Oct 12, 2022 (156)
69	EVA	ss5937546167	Oct 12, 2022 (156)
70	1000Genomes	NC_000001.10 - 68359887	Oct 11, 2018 (152)
71	1000Genomes_30x	NC_000001.11 - 67894204	Oct 12, 2022 (156)
72	The Avon Longitudinal Study of Parents and Children	NC_000001.10 - 68359887	Oct 11, 2018 (152)
73	Chileans	NC_000001.10 - 68359887	Apr 25, 2020 (154)
74	Genetic variation in the Estonian population	NC_000001.10 - 68359887	Oct 11, 2018 (152)
75	The Danish reference pan genome	NC_000001.10 - 68359887	Apr 25, 2020 (154)
76	gnomAD - Genomes	NC_000001.11 - 67894204	Apr 25, 2021 (155)
77	Genome of the Netherlands Release 5	NC_000001.10 - 68359887	Apr 25, 2020 (154)
78	HapMap	NC_000001.11 - 67894204	Apr 25, 2020 (154)
79	KOREAN population from KRGDB	NC_000001.10 - 68359887	Apr 25, 2020 (154)
80	Northern Sweden	NC_000001.10 - 68359887	Jul 12, 2019 (153)
81	Qatari	NC_000001.10 - 68359887	Apr 25, 2020 (154)
82	SGDP_PRJ	NC_000001.10 - 68359887	Apr 25, 2020 (154)
83	Siberian	NC_000001.10 - 68359887	Apr 25, 2020 (154)
84	8.3KJPN	NC_000001.10 - 68359887	Apr 25, 2021 (155)
85	14KJPN	NC_000001.11 - 67894204	Oct 12, 2022 (156)
86	TopMed	NC_000001.11 - 67894204	Apr 25, 2021 (155)
87	UK 10K study - Twins	NC_000001.10 - 68359887	Oct 11, 2018 (152)
88	A Vietnamese Genetic Variation Database	NC_000001.10 - 68359887	Jul 12, 2019 (153)
89	ALFA	NC_000001.11 - 67894204	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)
rs60862825	Feb 27, 2009 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss110589529, ss118773753, ss163480832, ss164481687, ss198574950, ss205094893, ss275862395, ss284066221, ss290530195, ss1584624047, ss1712340851	NC_000001.9:68132474:T:C	NC_000001.11:67894203:T:C	(self)
1981118, 1086026, 11179, 768626, 1539198, 463526, 1240767, 410719, 503734, 1051183, 280826, 2319789, 1086026, 227601, ss218434774, ss230571174, ss238258593, ss554213613, ss648089992, ss975254193, ss1067959392, ss1291249859, ss1425840012, ss1574124979, ss1600364561, ss1643358594, ss1794506607, ss1918461804, ss1966768346, ss2019748442, ss2147764472, ss2697682450, ss2756155898, ss2986959564, ss3343496209, ss3655030378, ss3727125854, ss3746315038, ss3783435219, ss3789089576, ss3793962313, ss3826218412, ss3849034203, ss3894063373, ss5144350482, ss5319298408, ss5505882587, ss5625706997, ss5832080282, ss5937546167	NC_000001.10:68359886:T:C	NC_000001.11:67894203:T:C	(self)
2537435, 13970199, 89294, 3074364, 16495736, 1681716103, ss2163249139, ss3023636204, ss3686947631, ss3799321542, ss4452889401, ss5242579470, ss5443611959, ss5515011500, ss5669237260, ss5800674316, ss5848944871, ss5908619366	NC_000001.11:67894203:T:C	NC_000001.11:67894203:T:C	(self)
ss18077628	NT_032977.6:29922955:T:C	NC_000001.11:67894203:T:C	(self)
ss23177273, ss43812514, ss66040662, ss75933606, ss82944826, ss106573356, ss155129438, ss161269972, ss169322178	NT_032977.9:38331804:T:C	NC_000001.11:67894203:T:C	(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 rs12025677

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

rs12025677