Name: rs12038117
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.

rs12038117

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:40192874 (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 / T>G
Variation Type: SNV Single Nucleotide Variation
Frequency: G=0.485300 (128454/264690, TOPMED)
G=0.485847 (67968/139896, GnomAD)
T=0.43999 (43296/98402, ALFA) (+ 19 more)
G=0.45584 (12881/28258, 14KJPN)
G=0.45459 (7619/16760, 8.3KJPN)
G=0.4535 (2904/6404, 1000G_30x)
G=0.4591 (2299/5008, 1000G)
T=0.3884 (1740/4480, Estonian)
T=0.4206 (1621/3854, ALSPAC)
T=0.4172 (1547/3708, TWINSUK)
T=0.4771 (1398/2930, KOREAN)
T=0.4952 (1032/2084, HGDP_Stanford)
G=0.4264 (805/1888, HapMap)
T=0.4743 (869/1832, Korea1K)
T=0.451 (450/998, GoNL)
T=0.430 (258/600, NorthernSweden)
T=0.302 (121/400, SGDP_PRJ)
T=0.356 (77/216, Qatari)
T=0.410 (87/212, Vietnamese)
T=0.25 (11/44, Siberian)
T=0.30 (12/40, GENOME_DK)
T=0.29 (4/14, Ancient Sardinia)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: RLF : 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	98402	T=0.43999	G=0.56001
European	Sub	76154	T=0.41012	G=0.58988
African	Sub	6520	T=0.7351	G=0.2649
African Others	Sub	236	T=0.822	G=0.178
African American	Sub	6284	T=0.7319	G=0.2681
Asian	Sub	522	T=0.483	G=0.517
East Asian	Sub	440	T=0.502	G=0.498
Other Asian	Sub	82	T=0.38	G=0.62
Latin American 1	Sub	682	T=0.490	G=0.510
Latin American 2	Sub	5534	T=0.4384	G=0.5616
South Asian	Sub	5020	T=0.4938	G=0.5062
Other	Sub	3970	T=0.4484	G=0.5516

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=0.514700	G=0.485300
gnomAD - Genomes	Global	Study-wide	139896	T=0.514153	G=0.485847
gnomAD - Genomes	European	Sub	75758	T=0.42229	G=0.57771
gnomAD - Genomes	African	Sub	41930	T=0.72585	G=0.27415
gnomAD - Genomes	American	Sub	13632	T=0.43229	G=0.56771
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	T=0.3168	G=0.6832
gnomAD - Genomes	East Asian	Sub	3106	T=0.4929	G=0.5071
gnomAD - Genomes	Other	Sub	2146	T=0.4772	G=0.5228
Allele Frequency Aggregator	Total	Global	98402	T=0.43999	G=0.56001
Allele Frequency Aggregator	European	Sub	76154	T=0.41012	G=0.58988
Allele Frequency Aggregator	African	Sub	6520	T=0.7351	G=0.2649
Allele Frequency Aggregator	Latin American 2	Sub	5534	T=0.4384	G=0.5616
Allele Frequency Aggregator	South Asian	Sub	5020	T=0.4938	G=0.5062
Allele Frequency Aggregator	Other	Sub	3970	T=0.4484	G=0.5516
Allele Frequency Aggregator	Latin American 1	Sub	682	T=0.490	G=0.510
Allele Frequency Aggregator	Asian	Sub	522	T=0.483	G=0.517
14KJPN	JAPANESE	Study-wide	28258	T=0.54416	G=0.45584
8.3KJPN	JAPANESE	Study-wide	16760	T=0.54541	G=0.45459
1000Genomes_30x	Global	Study-wide	6404	T=0.5465	G=0.4535
1000Genomes_30x	African	Sub	1786	T=0.7833	G=0.2167
1000Genomes_30x	Europe	Sub	1266	T=0.3989	G=0.6011
1000Genomes_30x	South Asian	Sub	1202	T=0.5042	G=0.4958
1000Genomes_30x	East Asian	Sub	1170	T=0.5017	G=0.4983
1000Genomes_30x	American	Sub	980	T=0.411	G=0.589
1000Genomes	Global	Study-wide	5008	T=0.5409	G=0.4591
1000Genomes	African	Sub	1322	T=0.7769	G=0.2231
1000Genomes	East Asian	Sub	1008	T=0.4950	G=0.5050
1000Genomes	Europe	Sub	1006	T=0.3907	G=0.6093
1000Genomes	South Asian	Sub	978	T=0.513	G=0.487
1000Genomes	American	Sub	694	T=0.415	G=0.585
Genetic variation in the Estonian population	Estonian	Study-wide	4480	T=0.3884	G=0.6116
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.4206	G=0.5794
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.4172	G=0.5828
KOREAN population from KRGDB	KOREAN	Study-wide	2930	T=0.4771	C=0.0000, G=0.5229
HGDP-CEPH-db Supplement 1	Global	Study-wide	2084	T=0.4952	G=0.5048
HGDP-CEPH-db Supplement 1	Est_Asia	Sub	470	T=0.474	G=0.526
HGDP-CEPH-db Supplement 1	Central_South_Asia	Sub	414	T=0.502	G=0.498
HGDP-CEPH-db Supplement 1	Middle_Est	Sub	350	T=0.389	G=0.611
HGDP-CEPH-db Supplement 1	Europe	Sub	320	T=0.409	G=0.591
HGDP-CEPH-db Supplement 1	Africa	Sub	242	T=0.798	G=0.202
HGDP-CEPH-db Supplement 1	America	Sub	216	T=0.426	G=0.574
HGDP-CEPH-db Supplement 1	Oceania	Sub	72	T=0.68	G=0.32
HapMap	Global	Study-wide	1888	T=0.5736	G=0.4264
HapMap	American	Sub	770	T=0.509	G=0.491
HapMap	African	Sub	688	T=0.714	G=0.286
HapMap	Asian	Sub	254	T=0.524	G=0.476
HapMap	Europe	Sub	176	T=0.381	G=0.619
Korean Genome Project	KOREAN	Study-wide	1832	T=0.4743	G=0.5257
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.451	G=0.549
Northern Sweden	ACPOP	Study-wide	600	T=0.430	G=0.570
SGDP_PRJ	Global	Study-wide	400	T=0.302	G=0.698
Qatari	Global	Study-wide	216	T=0.356	G=0.644
A Vietnamese Genetic Variation Database	Global	Study-wide	212	T=0.410	G=0.590
Siberian	Global	Study-wide	44	T=0.25	G=0.75
The Danish reference pan genome	Danish	Study-wide	40	T=0.30	G=0.70
Ancient Sardinia genome-wide 1240k capture data generation and analysis	Global	Study-wide	14	T=0.29	G=0.71

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.40192874T>C
GRCh38.p14 chr 1	NC_000001.11:g.40192874T>G
GRCh37.p13 chr 1	NC_000001.10:g.40658546T>C
GRCh37.p13 chr 1	NC_000001.10:g.40658546T>G

Gene: RLF, RLF zinc finger (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
RLF transcript	NM_012421.4:c.474+2021T>C	N/A	Intron Variant
RLF transcript variant X1	XM_047427055.1:c.	N/A	Genic Upstream Transcript Variant
RLF transcript variant X2	XM_047427057.1:c.	N/A	Genic Upstream Transcript 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	G
GRCh38.p14 chr 1	NC_000001.11:g.40192874=	NC_000001.11:g.40192874T>C	NC_000001.11:g.40192874T>G
GRCh37.p13 chr 1	NC_000001.10:g.40658546=	NC_000001.10:g.40658546T>C	NC_000001.10:g.40658546T>G
RLF transcript	NM_012421.3:c.474+2021=	NM_012421.3:c.474+2021T>C	NM_012421.3:c.474+2021T>G
RLF transcript	NM_012421.4:c.474+2021=	NM_012421.4:c.474+2021T>C	NM_012421.4:c.474+2021T>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, 22 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_SNP	ss18101361	Feb 28, 2004 (120)
2	ABI	ss44108682	Mar 14, 2006 (126)
3	ILLUMINA	ss66796981	Nov 29, 2006 (127)
4	ILLUMINA	ss66977315	Nov 29, 2006 (127)
5	ILLUMINA	ss67148728	Nov 29, 2006 (127)
6	ILLUMINA	ss70404047	May 16, 2007 (127)
7	ILLUMINA	ss70553108	May 23, 2008 (130)
8	ILLUMINA	ss71089312	May 16, 2007 (127)
9	ILLUMINA	ss75854592	Dec 06, 2007 (129)
10	HGSV	ss78897919	Dec 06, 2007 (129)
11	KRIBB_YJKIM	ss85175480	Dec 14, 2007 (130)
12	HUMANGENOME_JCVI	ss99202045	Feb 04, 2009 (130)
13	BGI	ss102736248	Dec 01, 2009 (131)
14	1000GENOMES	ss108142223	Jan 23, 2009 (130)
15	ILLUMINA-UK	ss118635996	Feb 14, 2009 (130)
16	ILLUMINA	ss121531069	Dec 01, 2009 (131)
17	ENSEMBL	ss139733049	Dec 01, 2009 (131)
18	ILLUMINA	ss153118483	Dec 01, 2009 (131)
19	GMI	ss154903233	Dec 01, 2009 (131)
20	ILLUMINA	ss159201060	Dec 01, 2009 (131)
21	ILLUMINA	ss160028103	Dec 01, 2009 (131)
22	ILLUMINA	ss170029820	Jul 04, 2010 (132)
23	ILLUMINA	ss171805440	Jul 04, 2010 (132)
24	BUSHMAN	ss198336738	Jul 04, 2010 (132)
25	BCM-HGSC-SUB	ss205388524	Jul 04, 2010 (132)
26	1000GENOMES	ss218338865	Jul 14, 2010 (132)
27	1000GENOMES	ss230501295	Jul 14, 2010 (132)
28	1000GENOMES	ss238202072	Jul 15, 2010 (132)
29	GMI	ss275793001	May 04, 2012 (137)
30	GMI	ss284036386	Apr 25, 2013 (138)
31	PJP	ss290810194	May 09, 2011 (134)
32	ILLUMINA	ss410897211	Sep 17, 2011 (135)
33	ILLUMINA	ss480178241	Sep 08, 2015 (146)
34	ILLUMINA	ss536748777	Sep 08, 2015 (146)
35	TISHKOFF	ss554005607	Apr 25, 2013 (138)
36	SSMP	ss647799181	Apr 25, 2013 (138)
37	ILLUMINA	ss825373355	Apr 01, 2015 (144)
38	ILLUMINA	ss832713514	Aug 21, 2014 (142)
39	ILLUMINA	ss833304270	Aug 21, 2014 (142)
40	EVA-GONL	ss975063510	Aug 21, 2014 (142)
41	JMKIDD_LAB	ss1067815714	Aug 21, 2014 (142)
42	1000GENOMES	ss1290499835	Aug 21, 2014 (142)
43	DDI	ss1425779822	Apr 01, 2015 (144)
44	EVA_GENOME_DK	ss1574004060	Apr 01, 2015 (144)
45	EVA_UK10K_ALSPAC	ss1599969383	Apr 01, 2015 (144)
46	EVA_UK10K_TWINSUK	ss1642963416	Apr 01, 2015 (144)
47	EVA_SVP	ss1712326107	Apr 01, 2015 (144)
48	WEILL_CORNELL_DGM	ss1918272980	Feb 12, 2016 (147)
49	GENOMED	ss1966726751	Jul 19, 2016 (147)
50	JJLAB	ss2019650128	Sep 14, 2016 (149)
51	USC_VALOUEV	ss2147661316	Dec 20, 2016 (150)
52	HUMAN_LONGEVITY	ss2161686061	Dec 20, 2016 (150)
53	GRF	ss2697569927	Nov 08, 2017 (151)
54	GNOMAD	ss2754014547	Nov 08, 2017 (151)
55	SWEGEN	ss2986656677	Nov 08, 2017 (151)
56	BIOINF_KMB_FNS_UNIBA	ss3023588040	Nov 08, 2017 (151)
57	CSHL	ss3343414314	Nov 08, 2017 (151)
58	ILLUMINA	ss3626075862	Oct 11, 2018 (152)
59	ILLUMINA	ss3635994902	Oct 11, 2018 (152)
60	ILLUMINA	ss3637750660	Oct 11, 2018 (152)
61	ILLUMINA	ss3638895057	Oct 11, 2018 (152)
62	ILLUMINA	ss3639444844	Oct 11, 2018 (152)
63	ILLUMINA	ss3642763373	Oct 11, 2018 (152)
64	URBANLAB	ss3646645293	Oct 11, 2018 (152)
65	EGCUT_WGS	ss3654721780	Jul 12, 2019 (153)
66	EVA_DECODE	ss3686579468	Jul 12, 2019 (153)
67	ACPOP	ss3726964696	Jul 12, 2019 (153)
68	EVA	ss3746082271	Jul 12, 2019 (153)
69	KHV_HUMAN_GENOMES	ss3799096875	Jul 12, 2019 (153)
70	EVA	ss3826125741	Apr 25, 2020 (154)
71	HGDP	ss3847330506	Apr 25, 2020 (154)
72	SGDP_PRJ	ss3848646953	Apr 25, 2020 (154)
73	KRGDB	ss3893616196	Apr 25, 2020 (154)
74	KOGIC	ss3944299539	Apr 25, 2020 (154)
75	EVA	ss3984790649	Apr 25, 2021 (155)
76	EVA	ss4016904913	Apr 25, 2021 (155)
77	TOPMED	ss4446204413	Apr 25, 2021 (155)
78	TOMMO_GENOMICS	ss5143487460	Apr 25, 2021 (155)
79	1000G_HIGH_COVERAGE	ss5241926187	Oct 13, 2022 (156)
80	HUGCELL_USP	ss5443028007	Oct 13, 2022 (156)
81	1000G_HIGH_COVERAGE	ss5514030806	Oct 13, 2022 (156)
82	SANFORD_IMAGENETICS	ss5625339432	Oct 13, 2022 (156)
83	TOMMO_GENOMICS	ss5668112445	Oct 13, 2022 (156)
84	YY_MCH	ss5800511253	Oct 13, 2022 (156)
85	EVA	ss5831828142	Oct 13, 2022 (156)
86	EVA	ss5848868788	Oct 13, 2022 (156)
87	EVA	ss5907864633	Oct 13, 2022 (156)
88	EVA	ss5937160995	Oct 13, 2022 (156)
89	1000Genomes	NC_000001.10 - 40658546	Oct 11, 2018 (152)
90	1000Genomes_30x	NC_000001.11 - 40192874	Oct 13, 2022 (156)
91	The Avon Longitudinal Study of Parents and Children	NC_000001.10 - 40658546	Oct 11, 2018 (152)
92	Genetic variation in the Estonian population	NC_000001.10 - 40658546	Oct 11, 2018 (152)
93	The Danish reference pan genome	NC_000001.10 - 40658546	Apr 25, 2020 (154)
94	gnomAD - Genomes	NC_000001.11 - 40192874	Apr 25, 2021 (155)
95	Genome of the Netherlands Release 5	NC_000001.10 - 40658546	Apr 25, 2020 (154)
96	HGDP-CEPH-db Supplement 1	NC_000001.9 - 40431133	Apr 25, 2020 (154)
97	HapMap	NC_000001.11 - 40192874	Apr 25, 2020 (154)
98	KOREAN population from KRGDB	NC_000001.10 - 40658546	Apr 25, 2020 (154)
99	Korean Genome Project	NC_000001.11 - 40192874	Apr 25, 2020 (154)
100	Northern Sweden	NC_000001.10 - 40658546	Jul 12, 2019 (153)
101	Ancient Sardinia genome-wide 1240k capture data generation and analysis	NC_000001.10 - 40658546	Apr 25, 2021 (155)
102	Qatari	NC_000001.10 - 40658546	Apr 25, 2020 (154)
103	SGDP_PRJ	NC_000001.10 - 40658546	Apr 25, 2020 (154)
104	Siberian	NC_000001.10 - 40658546	Apr 25, 2020 (154)
105	8.3KJPN	NC_000001.10 - 40658546	Apr 25, 2021 (155)
106	14KJPN	NC_000001.11 - 40192874	Oct 13, 2022 (156)
107	TopMed	NC_000001.11 - 40192874	Apr 25, 2021 (155)
108	UK 10K study - Twins	NC_000001.10 - 40658546	Oct 11, 2018 (152)
109	A Vietnamese Genetic Variation Database	NC_000001.10 - 40658546	Jul 12, 2019 (153)
110	ALFA	NC_000001.11 - 40192874	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)
rs57189322	May 23, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
793590, ss3893616196	NC_000001.10:40658545:T:C	NC_000001.11:40192873:T:C	(self)
ss78897919, ss3638895057, ss3639444844	NC_000001.8:40327638:T:G	NC_000001.11:40192873:T:G	(self)
8398, ss108142223, ss118635996, ss160028103, ss198336738, ss205388524, ss275793001, ss284036386, ss290810194, ss410897211, ss825373355, ss1712326107, ss3642763373, ss3847330506	NC_000001.9:40431132:T:G	NC_000001.11:40192873:T:G	(self)
1204276, 651063, 460028, 1466668, 278336, 793590, 249561, 16576, 314910, 663933, 177670, 1456767, 651063, 133874, ss218338865, ss230501295, ss238202072, ss480178241, ss536748777, ss554005607, ss647799181, ss832713514, ss833304270, ss975063510, ss1067815714, ss1290499835, ss1425779822, ss1574004060, ss1599969383, ss1642963416, ss1918272980, ss1966726751, ss2019650128, ss2147661316, ss2697569927, ss2754014547, ss2986656677, ss3343414314, ss3626075862, ss3635994902, ss3637750660, ss3654721780, ss3726964696, ss3746082271, ss3826125741, ss3848646953, ss3893616196, ss3984790649, ss4016904913, ss5143487460, ss5625339432, ss5831828142, ss5937160995	NC_000001.10:40658545:T:G	NC_000001.11:40192873:T:G	(self)
1556741, 8481746, 50499, 677540, 1949549, 9810748, 12392362044, ss2161686061, ss3023588040, ss3646645293, ss3686579468, ss3799096875, ss3944299539, ss4446204413, ss5241926187, ss5443028007, ss5514030806, ss5668112445, ss5800511253, ss5848868788, ss5907864633	NC_000001.11:40192873:T:G	NC_000001.11:40192873:T:G	(self)
ss18101361	NT_032977.6:2264992:T:G	NC_000001.11:40192873:T:G	(self)
ss44108682, ss66796981, ss66977315, ss67148728, ss70404047, ss70553108, ss71089312, ss75854592, ss85175480, ss99202045, ss102736248, ss121531069, ss139733049, ss153118483, ss154903233, ss159201060, ss170029820, ss171805440	NT_032977.9:10630463:T:G	NC_000001.11:40192873:T: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 rs12038117

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

rs12038117