Name: rs603412
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.

rs603412

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:20588925 (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>A / C>G
Variation Type: SNV Single Nucleotide Variation
Frequency: G=0.305981 (80990/264690, TOPMED)
G=0.314210 (44007/140056, GnomAD)
G=0.35897 (6781/18890, ALFA) (+ 17 more)
G=0.2359 (1511/6404, 1000G_30x)
G=0.2390 (1197/5008, 1000G)
G=0.3819 (1711/4480, Estonian)
G=0.4271 (1646/3854, ALSPAC)
G=0.4296 (1593/3708, TWINSUK)
G=0.2188 (641/2930, KOREAN)
G=0.2271 (416/1832, Korea1K)
G=0.423 (422/998, GoNL)
G=0.447 (268/600, NorthernSweden)
G=0.232 (124/534, MGP)
G=0.291 (138/474, PharmGKB)
G=0.242 (78/322, HapMap)
C=0.375 (96/256, SGDP_PRJ)
G=0.444 (96/216, Qatari)
G=0.083 (18/216, Vietnamese)
G=0.38 (15/40, GENOME_DK)
C=0.46 (13/28, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: CDA : 2KB Upstream 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	18890	C=0.64103	G=0.35897
European	Sub	14286	C=0.58253	G=0.41747
African	Sub	2946	C=0.9060	G=0.0940
African Others	Sub	114	C=0.974	G=0.026
African American	Sub	2832	C=0.9032	G=0.0968
Asian	Sub	112	C=0.786	G=0.214
East Asian	Sub	86	C=0.83	G=0.17
Other Asian	Sub	26	C=0.65	G=0.35
Latin American 1	Sub	146	C=0.671	G=0.329
Latin American 2	Sub	610	C=0.652	G=0.348
South Asian	Sub	98	C=0.69	G=0.31
Other	Sub	692	C=0.673	G=0.327

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=0.694019	G=0.305981
gnomAD - Genomes	Global	Study-wide	140056	C=0.685790	G=0.314210
gnomAD - Genomes	European	Sub	75826	C=0.58215	G=0.41785
gnomAD - Genomes	African	Sub	41990	C=0.89988	G=0.10012
gnomAD - Genomes	American	Sub	13640	C=0.61694	G=0.38306
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	C=0.5048	G=0.4952
gnomAD - Genomes	East Asian	Sub	3128	C=0.8200	G=0.1800
gnomAD - Genomes	Other	Sub	2148	C=0.6811	G=0.3189
Allele Frequency Aggregator	Total	Global	18890	C=0.64103	G=0.35897
Allele Frequency Aggregator	European	Sub	14286	C=0.58253	G=0.41747
Allele Frequency Aggregator	African	Sub	2946	C=0.9060	G=0.0940
Allele Frequency Aggregator	Other	Sub	692	C=0.673	G=0.327
Allele Frequency Aggregator	Latin American 2	Sub	610	C=0.652	G=0.348
Allele Frequency Aggregator	Latin American 1	Sub	146	C=0.671	G=0.329
Allele Frequency Aggregator	Asian	Sub	112	C=0.786	G=0.214
Allele Frequency Aggregator	South Asian	Sub	98	C=0.69	G=0.31
1000Genomes_30x	Global	Study-wide	6404	C=0.7641	G=0.2359
1000Genomes_30x	African	Sub	1786	C=0.9462	G=0.0538
1000Genomes_30x	Europe	Sub	1266	C=0.5900	G=0.4100
1000Genomes_30x	South Asian	Sub	1202	C=0.6988	G=0.3012
1000Genomes_30x	East Asian	Sub	1170	C=0.8376	G=0.1624
1000Genomes_30x	American	Sub	980	C=0.649	G=0.351
1000Genomes	Global	Study-wide	5008	C=0.7610	G=0.2390
1000Genomes	African	Sub	1322	C=0.9433	G=0.0567
1000Genomes	East Asian	Sub	1008	C=0.8304	G=0.1696
1000Genomes	Europe	Sub	1006	C=0.5915	G=0.4085
1000Genomes	South Asian	Sub	978	C=0.696	G=0.304
1000Genomes	American	Sub	694	C=0.650	G=0.350
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.6181	G=0.3819
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.5729	G=0.4271
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.5704	G=0.4296
KOREAN population from KRGDB	KOREAN	Study-wide	2930	C=0.7812	G=0.2188
Korean Genome Project	KOREAN	Study-wide	1832	C=0.7729	G=0.2271
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.577	G=0.423
Northern Sweden	ACPOP	Study-wide	600	C=0.553	G=0.447
Medical Genome Project healthy controls from Spanish population	Spanish controls	Study-wide	534	C=0.768	G=0.232
PharmGKB Aggregated	Global	Study-wide	474	C=0.709	G=0.291
PharmGKB Aggregated	PA153344364	Sub	240	C=0.713	G=0.287
PharmGKB Aggregated	PA153343416	Sub	234	C=0.705	G=0.295
HapMap	Global	Study-wide	322	C=0.758	G=0.242
HapMap	African	Sub	118	C=0.975	G=0.025
HapMap	American	Sub	116	C=0.543	G=0.457
HapMap	Asian	Sub	88	C=0.75	G=0.25
SGDP_PRJ	Global	Study-wide	256	C=0.375	G=0.625
Qatari	Global	Study-wide	216	C=0.556	G=0.444
A Vietnamese Genetic Variation Database	Global	Study-wide	216	C=0.917	G=0.083
The Danish reference pan genome	Danish	Study-wide	40	C=0.62	G=0.38
Siberian	Global	Study-wide	28	C=0.46	G=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.20588925C>A
GRCh38.p14 chr 1	NC_000001.11:g.20588925C>G
GRCh37.p13 chr 1	NC_000001.10:g.20915418C>A
GRCh37.p13 chr 1	NC_000001.10:g.20915418C>G

Gene: CDA, cytidine deaminase (plus strand) : 2KB Upstream Variant

Molecule type	Change	Amino acid[Codon]	SO Term
CDA transcript	NM_001785.3:c.	N/A	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	C=	A	G
GRCh38.p14 chr 1	NC_000001.11:g.20588925=	NC_000001.11:g.20588925C>A	NC_000001.11:g.20588925C>G
GRCh37.p13 chr 1	NC_000001.10:g.20915418=	NC_000001.10:g.20915418C>A	NC_000001.10:g.20915418C>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#.

93 SubSNP, 24 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_JCM	ss775420	Aug 11, 2000 (83)
2	KWOK	ss1084076	Oct 05, 2000 (92)
3	KWOK	ss1911679	Oct 18, 2000 (92)
4	KWOK	ss1912165	Oct 18, 2000 (98)
5	YUSUKE	ss2986758	Jun 15, 2001 (98)
6	HGBASE	ss3187728	Aug 15, 2001 (98)
7	TSC-CSHL	ss5197546	Oct 08, 2002 (108)
8	SC_SNP	ss13005261	Dec 05, 2003 (119)
9	SSAHASNP	ss20453026	Apr 05, 2004 (121)
10	ABI	ss44122951	Mar 14, 2006 (126)
11	ILLUMINA	ss65806294	Oct 16, 2006 (127)
12	SI_EXO	ss71641724	May 18, 2007 (127)
13	BCMHGSC_JDW	ss87282922	Mar 23, 2008 (129)
14	HUMANGENOME_JCVI	ss97923761	Feb 05, 2009 (130)
15	PHARMGKB_PPII	ss105109174	Feb 05, 2009 (130)
16	PHARMGKB_PPII	ss105109178	Feb 05, 2009 (130)
17	1000GENOMES	ss108046869	Jan 22, 2009 (130)
18	ENSEMBL	ss137834136	Dec 01, 2009 (131)
19	ENSEMBL	ss139083975	Dec 01, 2009 (131)
20	GMI	ss154737873	Dec 01, 2009 (131)
21	COMPLETE_GENOMICS	ss163939770	Jul 04, 2010 (132)
22	COMPLETE_GENOMICS	ss166207243	Jul 04, 2010 (132)
23	BUSHMAN	ss198135331	Jul 04, 2010 (132)
24	BCM-HGSC-SUB	ss205297545	Jul 04, 2010 (132)
25	1000GENOMES	ss230454693	Jul 14, 2010 (132)
26	1000GENOMES	ss238164310	Jul 15, 2010 (132)
27	GMI	ss275745355	May 04, 2012 (137)
28	GMI	ss284014829	Apr 25, 2013 (138)
29	PJP	ss290782024	May 09, 2011 (134)
30	ILLUMINA	ss482213725	May 04, 2012 (137)
31	ILLUMINA	ss483792045	May 04, 2012 (137)
32	ILLUMINA	ss535990337	Sep 08, 2015 (146)
33	TISHKOFF	ss553870183	Apr 25, 2013 (138)
34	SSMP	ss647626929	Apr 25, 2013 (138)
35	ILLUMINA	ss780410117	Aug 21, 2014 (142)
36	ILLUMINA	ss782339591	Aug 21, 2014 (142)
37	ILLUMINA	ss835899134	Aug 21, 2014 (142)
38	EVA-GONL	ss974926170	Aug 21, 2014 (142)
39	JMKIDD_LAB	ss1067721005	Aug 21, 2014 (142)
40	1000GENOMES	ss1289958117	Aug 21, 2014 (142)
41	DDI	ss1425738791	Apr 01, 2015 (144)
42	EVA_GENOME_DK	ss1573928856	Apr 01, 2015 (144)
43	EVA_DECODE	ss1584284367	Apr 01, 2015 (144)
44	EVA_UK10K_ALSPAC	ss1599686884	Apr 01, 2015 (144)
45	EVA_UK10K_TWINSUK	ss1642680917	Apr 01, 2015 (144)
46	EVA_MGP	ss1710893749	Apr 01, 2015 (144)
47	HAMMER_LAB	ss1794031204	Sep 08, 2015 (146)
48	WEILL_CORNELL_DGM	ss1918137909	Feb 12, 2016 (147)
49	GENOMED	ss1966700877	Jul 19, 2016 (147)
50	JJLAB	ss2019580711	Sep 14, 2016 (149)
51	USC_VALOUEV	ss2147584325	Dec 20, 2016 (150)
52	HUMAN_LONGEVITY	ss2160566517	Dec 20, 2016 (150)
53	ILLUMINA	ss2632487281	Nov 08, 2017 (151)
54	GRF	ss2697488853	Nov 08, 2017 (151)
55	GNOMAD	ss2752439838	Nov 08, 2017 (151)
56	AFFY	ss2985501210	Nov 08, 2017 (151)
57	SWEGEN	ss2986432877	Nov 08, 2017 (151)
58	BIOINF_KMB_FNS_UNIBA	ss3023555613	Nov 08, 2017 (151)
59	CSHL	ss3343357792	Nov 08, 2017 (151)
60	ILLUMINA	ss3626043581	Oct 11, 2018 (152)
61	ILLUMINA	ss3630525078	Oct 11, 2018 (152)
62	ILLUMINA	ss3641576826	Oct 11, 2018 (152)
63	URBANLAB	ss3646617399	Oct 11, 2018 (152)
64	EGCUT_WGS	ss3654503346	Jul 12, 2019 (153)
65	EVA_DECODE	ss3686305064	Jul 12, 2019 (153)
66	ACPOP	ss3726852118	Jul 12, 2019 (153)
67	EVA	ss3745916825	Jul 12, 2019 (153)
68	PACBIO	ss3783346872	Jul 12, 2019 (153)
69	PACBIO	ss3789017455	Jul 12, 2019 (153)
70	PACBIO	ss3793889927	Jul 12, 2019 (153)
71	KHV_HUMAN_GENOMES	ss3798936615	Jul 12, 2019 (153)
72	EVA	ss3826060480	Apr 25, 2020 (154)
73	SGDP_PRJ	ss3848364151	Apr 25, 2020 (154)
74	KRGDB	ss3893272947	Apr 25, 2020 (154)
75	KOGIC	ss3943989340	Apr 25, 2020 (154)
76	FSA-LAB	ss3983921142	Apr 27, 2021 (155)
77	TOPMED	ss4441458780	Apr 27, 2021 (155)
78	TOMMO_GENOMICS	ss5142833497	Apr 27, 2021 (155)
79	TOMMO_GENOMICS	ss5142833498	Apr 27, 2021 (155)
80	1000G_HIGH_COVERAGE	ss5241437937	Oct 12, 2022 (156)
81	EVA	ss5314599071	Oct 12, 2022 (156)
82	EVA	ss5317209353	Oct 12, 2022 (156)
83	HUGCELL_USP	ss5442595793	Oct 12, 2022 (156)
84	EVA	ss5505783644	Oct 12, 2022 (156)
85	1000G_HIGH_COVERAGE	ss5513313321	Oct 12, 2022 (156)
86	SANFORD_IMAGENETICS	ss5625073473	Oct 12, 2022 (156)
87	TOMMO_GENOMICS	ss5667240620	Oct 12, 2022 (156)
88	TOMMO_GENOMICS	ss5667240621	Oct 12, 2022 (156)
89	YY_MCH	ss5800394524	Oct 12, 2022 (156)
90	EVA	ss5831640920	Oct 12, 2022 (156)
91	EVA	ss5848814837	Oct 12, 2022 (156)
92	EVA	ss5907317287	Oct 12, 2022 (156)
93	EVA	ss5936889258	Oct 12, 2022 (156)
94	1000Genomes	NC_000001.10 - 20915418	Oct 11, 2018 (152)
95	1000Genomes_30x	NC_000001.11 - 20588925	Oct 12, 2022 (156)
96	The Avon Longitudinal Study of Parents and Children	NC_000001.10 - 20915418	Oct 11, 2018 (152)
97	Genetic variation in the Estonian population	NC_000001.10 - 20915418	Oct 11, 2018 (152)
98	The Danish reference pan genome	NC_000001.10 - 20915418	Apr 25, 2020 (154)
99	gnomAD - Genomes	NC_000001.11 - 20588925	Apr 27, 2021 (155)
100	Genome of the Netherlands Release 5	NC_000001.10 - 20915418	Apr 25, 2020 (154)
101	HapMap	NC_000001.11 - 20588925	Apr 25, 2020 (154)
102	KOREAN population from KRGDB	NC_000001.10 - 20915418	Apr 25, 2020 (154)
103	Korean Genome Project	NC_000001.11 - 20588925	Apr 25, 2020 (154)
104	Medical Genome Project healthy controls from Spanish population	NC_000001.10 - 20915418	Apr 25, 2020 (154)
105	Northern Sweden	NC_000001.10 - 20915418	Jul 12, 2019 (153)
106	PharmGKB Aggregated	NC_000001.11 - 20588925	Apr 25, 2020 (154)
107	Qatari	NC_000001.10 - 20915418	Apr 25, 2020 (154)
108	SGDP_PRJ	NC_000001.10 - 20915418	Apr 25, 2020 (154)
109	Siberian	NC_000001.10 - 20915418	Apr 25, 2020 (154)
110	8.3KJPN Submission ignored due to conflicting rows: Row 802804 (NC_000001.10:20915417:C:G 4504/16760) Row 802805 (NC_000001.10:20915417:C:A 2/16760)	-	Apr 27, 2021 (155)
111	8.3KJPN Submission ignored due to conflicting rows: Row 802804 (NC_000001.10:20915417:C:G 4504/16760) Row 802805 (NC_000001.10:20915417:C:A 2/16760)	-	Apr 27, 2021 (155)
112	14KJPN Submission ignored due to conflicting rows: Row 1077724 (NC_000001.11:20588924:C:G 7551/28258) Row 1077725 (NC_000001.11:20588924:C:A 2/28258)	-	Oct 12, 2022 (156)
113	14KJPN Submission ignored due to conflicting rows: Row 1077724 (NC_000001.11:20588924:C:G 7551/28258) Row 1077725 (NC_000001.11:20588924:C:A 2/28258)	-	Oct 12, 2022 (156)
114	TopMed	NC_000001.11 - 20588925	Apr 27, 2021 (155)
115	UK 10K study - Twins	NC_000001.10 - 20915418	Oct 11, 2018 (152)
116	A Vietnamese Genetic Variation Database	NC_000001.10 - 20915418	Jul 12, 2019 (153)
117	ALFA	NC_000001.11 - 20588925	Apr 27, 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)
rs818366	Jan 18, 2001 (92)
rs1254017	Aug 15, 2001 (98)
rs2072670	Aug 15, 2001 (98)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss5142833498	NC_000001.10:20915417:C:A	NC_000001.11:20588924:C:A	(self)
ss5667240621	NC_000001.11:20588924:C:A	NC_000001.11:20588924:C:A
ss87282922, ss108046869, ss163939770, ss166207243, ss198135331, ss205297545, ss275745355, ss284014829, ss290782024, ss482213725, ss1584284367	NC_000001.9:20788004:C:G	NC_000001.11:20588924:C:G	(self)
643316, 339242, 241594, 1418151, 147387, 450341, 10501, 136983, 179839, 381131, 100679, 339242, 72714, ss230454693, ss238164310, ss483792045, ss535990337, ss553870183, ss647626929, ss780410117, ss782339591, ss835899134, ss974926170, ss1067721005, ss1289958117, ss1425738791, ss1573928856, ss1599686884, ss1642680917, ss1710893749, ss1794031204, ss1918137909, ss1966700877, ss2019580711, ss2147584325, ss2632487281, ss2697488853, ss2752439838, ss2985501210, ss2986432877, ss3343357792, ss3626043581, ss3630525078, ss3641576826, ss3654503346, ss3726852118, ss3745916825, ss3783346872, ss3789017455, ss3793889927, ss3826060480, ss3848364151, ss3893272947, ss3983921142, ss5142833497, ss5314599071, ss5317209353, ss5505783644, ss5625073473, ss5831640920, ss5936889258	NC_000001.10:20915417:C:G	NC_000001.11:20588924:C:G	(self)
839256, 4465027, 26562, 367341, 183, 5065115, 463092674, ss2160566517, ss3023555613, ss3646617399, ss3686305064, ss3798936615, ss3943989340, ss4441458780, ss5241437937, ss5442595793, ss5513313321, ss5667240620, ss5800394524, ss5848814837, ss5907317287	NC_000001.11:20588924:C:G	NC_000001.11:20588924:C:G	(self)
ss13005261	NT_004610.15:1718667:C:G	NC_000001.11:20588924:C:G	(self)
ss20453026	NT_004610.16:1718667:C:G	NC_000001.11:20588924:C:G	(self)
ss775420, ss1084076, ss1911679, ss1912165, ss2986758, ss3187728, ss5197546, ss44122951, ss65806294, ss71641724, ss97923761, ss105109174, ss105109178, ss137834136, ss139083975, ss154737873	NT_004610.19:7595505:C:G	NC_000001.11:20588924:C: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 rs603412

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

rs603412