Name: rs2345978
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.

rs2345978

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr6:62474608 (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: A>G / A>T
Variation Type: SNV Single Nucleotide Variation
Frequency: A=0.318006 (84173/264690, TOPMED)
A=0.300540 (42069/139978, GnomAD)
A=0.44847 (12673/28258, 14KJPN) (+ 16 more)
A=0.33331 (5935/17806, ALFA)
A=0.45179 (7572/16760, 8.3KJPN)
A=0.3343 (2141/6404, 1000G_30x)
A=0.3391 (1698/5008, 1000G)
A=0.2891 (1295/4480, Estonian)
A=0.3731 (1438/3854, ALSPAC)
A=0.3679 (1364/3708, TWINSUK)
A=0.4270 (1251/2930, KOREAN)
A=0.4498 (824/1832, Korea1K)
A=0.401 (400/998, GoNL)
A=0.413 (248/600, NorthernSweden)
A=0.283 (126/446, SGDP_PRJ)
G=0.491 (106/216, Qatari)
A=0.402 (86/214, Vietnamese)
A=0.31 (13/42, Siberian)
A=0.40 (16/40, GENOME_DK)

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	17806	A=0.33331	G=0.66669, T=0.00000
European	Sub	13718	A=0.35158	G=0.64842, T=0.00000
African	Sub	2434	A=0.1504	G=0.8496, T=0.0000
African Others	Sub	90	A=0.10	G=0.90, T=0.00
African American	Sub	2344	A=0.1523	G=0.8477, T=0.0000
Asian	Sub	112	A=0.482	G=0.518, T=0.000
East Asian	Sub	86	A=0.50	G=0.50, T=0.00
Other Asian	Sub	26	A=0.42	G=0.58, T=0.00
Latin American 1	Sub	146	A=0.349	G=0.651, T=0.000
Latin American 2	Sub	610	A=0.551	G=0.449, T=0.000
South Asian	Sub	98	A=0.52	G=0.48, T=0.00
Other	Sub	688	A=0.369	G=0.631, 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
TopMed	Global	Study-wide	264690	A=0.318006	G=0.681994
gnomAD - Genomes	Global	Study-wide	139978	A=0.300540	G=0.699460
gnomAD - Genomes	European	Sub	75796	A=0.34858	G=0.65142
gnomAD - Genomes	African	Sub	41966	A=0.14843	G=0.85157
gnomAD - Genomes	American	Sub	13622	A=0.43958	G=0.56042
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	A=0.4049	G=0.5951
gnomAD - Genomes	East Asian	Sub	3122	A=0.4407	G=0.5593
gnomAD - Genomes	Other	Sub	2148	A=0.3301	G=0.6699
14KJPN	JAPANESE	Study-wide	28258	A=0.44847	G=0.55153
Allele Frequency Aggregator	Total	Global	17806	A=0.33331	G=0.66669, T=0.00000
Allele Frequency Aggregator	European	Sub	13718	A=0.35158	G=0.64842, T=0.00000
Allele Frequency Aggregator	African	Sub	2434	A=0.1504	G=0.8496, T=0.0000
Allele Frequency Aggregator	Other	Sub	688	A=0.369	G=0.631, T=0.000
Allele Frequency Aggregator	Latin American 2	Sub	610	A=0.551	G=0.449, T=0.000
Allele Frequency Aggregator	Latin American 1	Sub	146	A=0.349	G=0.651, T=0.000
Allele Frequency Aggregator	Asian	Sub	112	A=0.482	G=0.518, T=0.000
Allele Frequency Aggregator	South Asian	Sub	98	A=0.52	G=0.48, T=0.00
8.3KJPN	JAPANESE	Study-wide	16760	A=0.45179	G=0.54821
1000Genomes_30x	Global	Study-wide	6404	A=0.3343	G=0.6657
1000Genomes_30x	African	Sub	1786	A=0.0985	G=0.9015
1000Genomes_30x	Europe	Sub	1266	A=0.3539	G=0.6461
1000Genomes_30x	South Asian	Sub	1202	A=0.4501	G=0.5499
1000Genomes_30x	East Asian	Sub	1170	A=0.4085	G=0.5915
1000Genomes_30x	American	Sub	980	A=0.508	G=0.492
1000Genomes	Global	Study-wide	5008	A=0.3391	G=0.6609
1000Genomes	African	Sub	1322	A=0.1014	G=0.8986
1000Genomes	East Asian	Sub	1008	A=0.4087	G=0.5913
1000Genomes	Europe	Sub	1006	A=0.3529	G=0.6471
1000Genomes	South Asian	Sub	978	A=0.456	G=0.544
1000Genomes	American	Sub	694	A=0.506	G=0.494
Genetic variation in the Estonian population	Estonian	Study-wide	4480	A=0.2891	G=0.7109
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.3731	G=0.6269
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.3679	G=0.6321
KOREAN population from KRGDB	KOREAN	Study-wide	2930	A=0.4270	G=0.5730
Korean Genome Project	KOREAN	Study-wide	1832	A=0.4498	G=0.5502
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	A=0.401	G=0.599
Northern Sweden	ACPOP	Study-wide	600	A=0.413	G=0.587
SGDP_PRJ	Global	Study-wide	446	A=0.283	G=0.717
Qatari	Global	Study-wide	216	A=0.509	G=0.491
A Vietnamese Genetic Variation Database	Global	Study-wide	214	A=0.402	G=0.598
Siberian	Global	Study-wide	42	A=0.31	G=0.69
The Danish reference pan genome	Danish	Study-wide	40	A=0.40	G=0.60

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 6	NC_000006.12:g.62474608A>G
GRCh38.p14 chr 6	NC_000006.12:g.62474608A>T
GRCh37.p13 chr 6	NC_000006.11:g.63184513A>G
GRCh37.p13 chr 6	NC_000006.11:g.63184513A>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	A=	G	T
GRCh38.p14 chr 6	NC_000006.12:g.62474608=	NC_000006.12:g.62474608A>G	NC_000006.12:g.62474608A>T
GRCh37.p13 chr 6	NC_000006.11:g.63184513=	NC_000006.11:g.63184513A>G	NC_000006.11:g.63184513A>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#.

74 SubSNP, 19 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	TSC-CSHL	ss3300035	Sep 28, 2001 (100)
2	SC_SNP	ss12779037	Dec 05, 2003 (119)
3	CSHL-HAPMAP	ss17892613	Feb 27, 2004 (120)
4	SSAHASNP	ss22372064	Apr 05, 2004 (123)
5	ABI	ss42751068	Mar 14, 2006 (126)
6	HGSV	ss78703956	Dec 06, 2007 (129)
7	HGSV	ss84708680	Dec 16, 2007 (130)
8	BCMHGSC_JDW	ss93475882	Mar 24, 2008 (129)
9	HUMANGENOME_JCVI	ss98398886	Feb 06, 2009 (130)
10	BGI	ss106004930	Feb 06, 2009 (130)
11	ILLUMINA-UK	ss116501048	Dec 01, 2009 (131)
12	ENSEMBL	ss143729991	Dec 01, 2009 (131)
13	COMPLETE_GENOMICS	ss162430052	Jul 04, 2010 (132)
14	COMPLETE_GENOMICS	ss163605245	Jul 04, 2010 (132)
15	COMPLETE_GENOMICS	ss166791653	Jul 04, 2010 (132)
16	BUSHMAN	ss201916866	Jul 04, 2010 (132)
17	BCM-HGSC-SUB	ss207850733	Jul 04, 2010 (132)
18	1000GENOMES	ss233498633	Jul 14, 2010 (132)
19	1000GENOMES	ss240550205	Jul 15, 2010 (132)
20	BL	ss254395899	May 09, 2011 (134)
21	GMI	ss278831617	May 04, 2012 (137)
22	GMI	ss285422543	Apr 25, 2013 (138)
23	PJP	ss293617431	May 09, 2011 (134)
24	TISHKOFF	ss559244198	Apr 25, 2013 (138)
25	SSMP	ss653192480	Apr 25, 2013 (138)
26	EVA-GONL	ss983001820	Aug 21, 2014 (142)
27	JMKIDD_LAB	ss1073664706	Aug 21, 2014 (142)
28	1000GENOMES	ss1320403520	Aug 21, 2014 (142)
29	DDI	ss1430752374	Apr 01, 2015 (144)
30	EVA_GENOME_DK	ss1581701062	Apr 01, 2015 (144)
31	EVA_DECODE	ss1592538782	Apr 01, 2015 (144)
32	EVA_UK10K_ALSPAC	ss1615710263	Apr 01, 2015 (144)
33	EVA_UK10K_TWINSUK	ss1658704296	Apr 01, 2015 (144)
34	HAMMER_LAB	ss1804465752	Sep 08, 2015 (146)
35	WEILL_CORNELL_DGM	ss1926260575	Feb 12, 2016 (147)
36	GENOMED	ss1970413252	Jul 19, 2016 (147)
37	JJLAB	ss2023770139	Sep 14, 2016 (149)
38	USC_VALOUEV	ss2151961573	Dec 20, 2016 (150)
39	SYSTEMSBIOZJU	ss2626378538	Nov 08, 2017 (151)
40	GRF	ss2707566489	Nov 08, 2017 (151)
41	GNOMAD	ss2839747979	Nov 08, 2017 (151)
42	SWEGEN	ss2999192017	Nov 08, 2017 (151)
43	BIOINF_KMB_FNS_UNIBA	ss3025676276	Nov 08, 2017 (151)
44	CSHL	ss3347007087	Nov 08, 2017 (151)
45	URBANLAB	ss3648366528	Oct 12, 2018 (152)
46	EGCUT_WGS	ss3667053477	Jul 13, 2019 (153)
47	EVA_DECODE	ss3717347398	Jul 13, 2019 (153)
48	ACPOP	ss3733564510	Jul 13, 2019 (153)
49	EVA	ss3765100888	Jul 13, 2019 (153)
50	PACBIO	ss3785493777	Jul 13, 2019 (153)
51	PACBIO	ss3790841411	Jul 13, 2019 (153)
52	PACBIO	ss3795720434	Jul 13, 2019 (153)
53	KHV_HUMAN_GENOMES	ss3808248777	Jul 13, 2019 (153)
54	EVA	ss3829957440	Apr 26, 2020 (154)
55	EVA	ss3838456590	Apr 26, 2020 (154)
56	EVA	ss3843903165	Apr 26, 2020 (154)
57	SGDP_PRJ	ss3864727585	Apr 26, 2020 (154)
58	KRGDB	ss3911577545	Apr 26, 2020 (154)
59	KOGIC	ss3959189531	Apr 26, 2020 (154)
60	TOPMED	ss4705443831	Apr 26, 2021 (155)
61	TOMMO_GENOMICS	ss5177813483	Apr 26, 2021 (155)
62	1000G_HIGH_COVERAGE	ss5268699697	Oct 17, 2022 (156)
63	EVA	ss5366054417	Oct 17, 2022 (156)
64	HUGCELL_USP	ss5466321140	Oct 17, 2022 (156)
65	EVA	ss5508521626	Oct 17, 2022 (156)
66	1000G_HIGH_COVERAGE	ss5554749124	Oct 17, 2022 (156)
67	SANFORD_IMAGENETICS	ss5640541409	Oct 17, 2022 (156)
68	TOMMO_GENOMICS	ss5716096326	Oct 17, 2022 (156)
69	YY_MCH	ss5807539644	Oct 17, 2022 (156)
70	EVA	ss5842345821	Oct 17, 2022 (156)
71	EVA	ss5855383554	Oct 17, 2022 (156)
72	EVA	ss5884082561	Oct 17, 2022 (156)
73	EVA	ss5969033028	Oct 17, 2022 (156)
74	EVA	ss5980373009	Oct 17, 2022 (156)
75	1000Genomes	NC_000006.11 - 63184513	Oct 12, 2018 (152)
76	1000Genomes_30x	NC_000006.12 - 62474608	Oct 17, 2022 (156)
77	The Avon Longitudinal Study of Parents and Children	NC_000006.11 - 63184513	Oct 12, 2018 (152)
78	Genetic variation in the Estonian population	NC_000006.11 - 63184513	Oct 12, 2018 (152)
79	The Danish reference pan genome	NC_000006.11 - 63184513	Apr 26, 2020 (154)
80	gnomAD - Genomes	NC_000006.12 - 62474608	Apr 26, 2021 (155)
81	Genome of the Netherlands Release 5	NC_000006.11 - 63184513	Apr 26, 2020 (154)
82	KOREAN population from KRGDB	NC_000006.11 - 63184513	Apr 26, 2020 (154)
83	Korean Genome Project	NC_000006.12 - 62474608	Apr 26, 2020 (154)
84	Northern Sweden	NC_000006.11 - 63184513	Jul 13, 2019 (153)
85	Qatari	NC_000006.11 - 63184513	Apr 26, 2020 (154)
86	SGDP_PRJ	NC_000006.11 - 63184513	Apr 26, 2020 (154)
87	Siberian	NC_000006.11 - 63184513	Apr 26, 2020 (154)
88	8.3KJPN	NC_000006.11 - 63184513	Apr 26, 2021 (155)
89	14KJPN	NC_000006.12 - 62474608	Oct 17, 2022 (156)
90	TopMed	NC_000006.12 - 62474608	Apr 26, 2021 (155)
91	UK 10K study - Twins	NC_000006.11 - 63184513	Oct 12, 2018 (152)
92	A Vietnamese Genetic Variation Database	NC_000006.11 - 63184513	Jul 13, 2019 (153)
93	ALFA	NC_000006.12 - 62474608	Apr 26, 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)
rs13191603	Sep 24, 2004 (123)
rs61544949	May 27, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss78703956, ss84708680	NC_000006.9:63242471:A:G	NC_000006.12:62474607:A:G	(self)
ss93475882, ss116501048, ss162430052, ss163605245, ss166791653, ss201916866, ss207850733, ss254395899, ss278831617, ss285422543, ss293617431, ss1592538782	NC_000006.10:63242471:A:G	NC_000006.12:62474607:A:G	(self)
32201408, 17943679, 12791725, 7866001, 7989475, 18754939, 6849375, 8302505, 16744565, 4477927, 35782790, 17943679, 3982377, ss233498633, ss240550205, ss559244198, ss653192480, ss983001820, ss1073664706, ss1320403520, ss1430752374, ss1581701062, ss1615710263, ss1658704296, ss1804465752, ss1926260575, ss1970413252, ss2023770139, ss2151961573, ss2626378538, ss2707566489, ss2839747979, ss2999192017, ss3347007087, ss3667053477, ss3733564510, ss3765100888, ss3785493777, ss3790841411, ss3795720434, ss3829957440, ss3838456590, ss3864727585, ss3911577545, ss5177813483, ss5366054417, ss5508521626, ss5640541409, ss5842345821, ss5969033028, ss5980373009	NC_000006.11:63184512:A:G	NC_000006.12:62474607:A:G	(self)
42275059, 227290733, 15567532, 49933430, 542821389, 9425821503, ss3025676276, ss3648366528, ss3717347398, ss3808248777, ss3843903165, ss3959189531, ss4705443831, ss5268699697, ss5466321140, ss5554749124, ss5716096326, ss5807539644, ss5855383554, ss5884082561	NC_000006.12:62474607:A:G	NC_000006.12:62474607:A:G	(self)
ss12779037, ss17892613, ss22372064	NT_007299.12:1005923:A:G	NC_000006.12:62474607:A:G	(self)
ss3300035, ss42751068, ss98398886, ss106004930, ss143729991	NT_007299.13:1304346:A:G	NC_000006.12:62474607:A:G	(self)
9425821503	NC_000006.12:62474607:A:T	NC_000006.12:62474607:A: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 rs2345978

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

rs2345978