Name: rs4709898
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.

rs4709898

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr6:164794710 (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>T
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.260414 (68929/264690, TOPMED)
T=0.243212 (34021/139882, GnomAD)
T=0.30101 (8506/28258, 14KJPN) (+ 19 more)
T=0.24376 (5588/22924, ALFA)
T=0.30453 (5104/16760, 8.3KJPN)
T=0.3270 (2094/6404, 1000G_30x)
T=0.3257 (1631/5008, 1000G)
T=0.2167 (971/4480, Estonian)
T=0.2159 (832/3854, ALSPAC)
T=0.2071 (768/3708, TWINSUK)
T=0.3096 (907/2930, KOREAN)
T=0.2817 (516/1832, Korea1K)
T=0.3030 (543/1792, HapMap)
T=0.249 (249/998, GoNL)
T=0.334 (209/626, Chileans)
T=0.188 (113/600, NorthernSweden)
C=0.337 (91/270, SGDP_PRJ)
T=0.259 (56/216, Qatari)
T=0.300 (63/210, Vietnamese)
T=0.23 (16/70, Ancient Sardinia)
T=0.20 (8/40, GENOME_DK)
C=0.45 (10/22, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: MEAT6 : 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	22924	C=0.75624	T=0.24376
European	Sub	16012	C=0.78766	T=0.21234
African	Sub	2946	C=0.7315	T=0.2685
African Others	Sub	114	C=0.684	T=0.316
African American	Sub	2832	C=0.7334	T=0.2666
Asian	Sub	112	C=0.688	T=0.312
East Asian	Sub	86	C=0.69	T=0.31
Other Asian	Sub	26	C=0.69	T=0.31
Latin American 1	Sub	226	C=0.783	T=0.217
Latin American 2	Sub	2622	C=0.6022	T=0.3978
South Asian	Sub	98	C=0.62	T=0.38
Other	Sub	908	C=0.743	T=0.257

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=0.739586	T=0.260414
gnomAD - Genomes	Global	Study-wide	139882	C=0.756788	T=0.243212
gnomAD - Genomes	European	Sub	75780	C=0.78794	T=0.21206
gnomAD - Genomes	African	Sub	41884	C=0.72658	T=0.27342
gnomAD - Genomes	American	Sub	13628	C=0.67919	T=0.32081
gnomAD - Genomes	Ashkenazi Jewish	Sub	3316	C=0.8085	T=0.1915
gnomAD - Genomes	East Asian	Sub	3126	C=0.6993	T=0.3007
gnomAD - Genomes	Other	Sub	2148	C=0.7430	T=0.2570
14KJPN	JAPANESE	Study-wide	28258	C=0.69899	T=0.30101
Allele Frequency Aggregator	Total	Global	22924	C=0.75624	T=0.24376
Allele Frequency Aggregator	European	Sub	16012	C=0.78766	T=0.21234
Allele Frequency Aggregator	African	Sub	2946	C=0.7315	T=0.2685
Allele Frequency Aggregator	Latin American 2	Sub	2622	C=0.6022	T=0.3978
Allele Frequency Aggregator	Other	Sub	908	C=0.743	T=0.257
Allele Frequency Aggregator	Latin American 1	Sub	226	C=0.783	T=0.217
Allele Frequency Aggregator	Asian	Sub	112	C=0.688	T=0.312
Allele Frequency Aggregator	South Asian	Sub	98	C=0.62	T=0.38
8.3KJPN	JAPANESE	Study-wide	16760	C=0.69547	T=0.30453
1000Genomes_30x	Global	Study-wide	6404	C=0.6730	T=0.3270
1000Genomes_30x	African	Sub	1786	C=0.7128	T=0.2872
1000Genomes_30x	Europe	Sub	1266	C=0.7852	T=0.2148
1000Genomes_30x	South Asian	Sub	1202	C=0.5649	T=0.4351
1000Genomes_30x	East Asian	Sub	1170	C=0.6709	T=0.3291
1000Genomes_30x	American	Sub	980	C=0.591	T=0.409
1000Genomes	Global	Study-wide	5008	C=0.6743	T=0.3257
1000Genomes	African	Sub	1322	C=0.7065	T=0.2935
1000Genomes	East Asian	Sub	1008	C=0.6796	T=0.3204
1000Genomes	Europe	Sub	1006	C=0.7913	T=0.2087
1000Genomes	South Asian	Sub	978	C=0.561	T=0.439
1000Genomes	American	Sub	694	C=0.595	T=0.405
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.7833	T=0.2167
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.7841	T=0.2159
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.7929	T=0.2071
KOREAN population from KRGDB	KOREAN	Study-wide	2930	C=0.6904	A=0.0000, T=0.3096
Korean Genome Project	KOREAN	Study-wide	1832	C=0.7183	T=0.2817
HapMap	Global	Study-wide	1792	C=0.6970	T=0.3030
HapMap	African	Sub	692	C=0.699	T=0.301
HapMap	American	Sub	670	C=0.682	T=0.318
HapMap	Asian	Sub	254	C=0.673	T=0.327
HapMap	Europe	Sub	176	C=0.778	T=0.222
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.751	T=0.249
Chileans	Chilean	Study-wide	626	C=0.666	T=0.334
Northern Sweden	ACPOP	Study-wide	600	C=0.812	T=0.188
SGDP_PRJ	Global	Study-wide	270	C=0.337	T=0.663
Qatari	Global	Study-wide	216	C=0.741	T=0.259
A Vietnamese Genetic Variation Database	Global	Study-wide	210	C=0.700	T=0.300
Ancient Sardinia genome-wide 1240k capture data generation and analysis	Global	Study-wide	70	C=0.77	T=0.23
The Danish reference pan genome	Danish	Study-wide	40	C=0.80	T=0.20
Siberian	Global	Study-wide	22	C=0.45	T=0.55

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.164794710C>A
GRCh38.p14 chr 6	NC_000006.12:g.164794710C>T
GRCh37.p13 chr 6	NC_000006.11:g.165208199C>A
GRCh37.p13 chr 6	NC_000006.11:g.165208199C>T

Gene: MEAT6, melanoma-associated transcript 6 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
MEAT6 transcript	NR_131926.1: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	C=	A	T
GRCh38.p14 chr 6	NC_000006.12:g.164794710=	NC_000006.12:g.164794710C>A	NC_000006.12:g.164794710C>T
GRCh37.p13 chr 6	NC_000006.11:g.165208199=	NC_000006.11:g.165208199C>A	NC_000006.11:g.165208199C>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#.

77 SubSNP, 22 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	WI_SSAHASNP	ss6489685	Feb 20, 2003 (111)
2	SC_SNP	ss12793129	Dec 05, 2003 (119)
3	PERLEGEN	ss23676424	Sep 20, 2004 (123)
4	ABI	ss44710591	Mar 14, 2006 (126)
5	AFFY	ss66162482	Nov 30, 2006 (127)
6	AFFY	ss76206889	Dec 08, 2007 (129)
7	KRIBB_YJKIM	ss82097565	Dec 15, 2007 (130)
8	HUMANGENOME_JCVI	ss98560997	Feb 05, 2009 (130)
9	1000GENOMES	ss111284790	Jan 25, 2009 (130)
10	ILLUMINA-UK	ss116812312	Feb 14, 2009 (130)
11	ENSEMBL	ss143119157	Dec 01, 2009 (131)
12	GMI	ss157871882	Dec 01, 2009 (131)
13	COMPLETE_GENOMICS	ss162970626	Jul 04, 2010 (132)
14	AFFY	ss172811066	Jul 04, 2010 (132)
15	BUSHMAN	ss202733461	Jul 04, 2010 (132)
16	1000GENOMES	ss211964425	Jul 14, 2010 (132)
17	1000GENOMES	ss222816539	Jul 14, 2010 (132)
18	1000GENOMES	ss233783397	Jul 15, 2010 (132)
19	1000GENOMES	ss240777336	Jul 15, 2010 (132)
20	BL	ss254795043	May 09, 2011 (134)
21	GMI	ss279119402	May 04, 2012 (137)
22	GMI	ss285547626	Apr 25, 2013 (138)
23	PJP	ss293783434	May 09, 2011 (134)
24	TISHKOFF	ss559693607	Apr 25, 2013 (138)
25	SSMP	ss654036843	Apr 25, 2013 (138)
26	EVA-GONL	ss983767243	Aug 21, 2014 (142)
27	JMKIDD_LAB	ss1074235392	Aug 21, 2014 (142)
28	1000GENOMES	ss1323282917	Aug 21, 2014 (142)
29	DDI	ss1430971453	Apr 01, 2015 (144)
30	EVA_GENOME_DK	ss1581999772	Apr 01, 2015 (144)
31	EVA_DECODE	ss1593343550	Apr 01, 2015 (144)
32	EVA_UK10K_ALSPAC	ss1617243324	Apr 01, 2015 (144)
33	EVA_UK10K_TWINSUK	ss1660237357	Apr 01, 2015 (144)
34	EVA_SVP	ss1712919929	Apr 01, 2015 (144)
35	HAMMER_LAB	ss1804788562	Sep 08, 2015 (146)
36	WEILL_CORNELL_DGM	ss1927008396	Feb 12, 2016 (147)
37	GENOMED	ss1970584853	Jul 19, 2016 (147)
38	JJLAB	ss2024172137	Sep 14, 2016 (149)
39	USC_VALOUEV	ss2152366414	Dec 20, 2016 (150)
40	HUMAN_LONGEVITY	ss2290477880	Dec 20, 2016 (150)
41	SYSTEMSBIOZJU	ss2626576378	Nov 08, 2017 (151)
42	GRF	ss2708007121	Nov 08, 2017 (151)
43	GNOMAD	ss2847961383	Nov 08, 2017 (151)
44	SWEGEN	ss3000354862	Nov 08, 2017 (151)
45	BIOINF_KMB_FNS_UNIBA	ss3025878580	Nov 08, 2017 (151)
46	CSHL	ss3347346672	Nov 08, 2017 (151)
47	URBANLAB	ss3648524013	Oct 12, 2018 (152)
48	EGCUT_WGS	ss3668296005	Jul 13, 2019 (153)
49	EVA_DECODE	ss3718776482	Jul 13, 2019 (153)
50	ACPOP	ss3734207250	Jul 13, 2019 (153)
51	EVA	ss3765983366	Jul 13, 2019 (153)
52	PACBIO	ss3785687904	Jul 13, 2019 (153)
53	PACBIO	ss3791004803	Jul 13, 2019 (153)
54	PACBIO	ss3795884281	Jul 13, 2019 (153)
55	KHV_HUMAN_GENOMES	ss3809148121	Jul 13, 2019 (153)
56	EVA	ss3830324197	Apr 26, 2020 (154)
57	EVA	ss3838647178	Apr 26, 2020 (154)
58	EVA	ss3844097572	Apr 26, 2020 (154)
59	SGDP_PRJ	ss3866246485	Apr 26, 2020 (154)
60	KRGDB	ss3913241098	Apr 26, 2020 (154)
61	KOGIC	ss3960562665	Apr 26, 2020 (154)
62	EVA	ss3985268776	Apr 26, 2021 (155)
63	TOPMED	ss4730403977	Apr 26, 2021 (155)
64	TOMMO_GENOMICS	ss5181059538	Apr 26, 2021 (155)
65	1000G_HIGH_COVERAGE	ss5271238976	Oct 13, 2022 (156)
66	EVA	ss5370627617	Oct 13, 2022 (156)
67	HUGCELL_USP	ss5468601401	Oct 13, 2022 (156)
68	EVA	ss5508796880	Oct 13, 2022 (156)
69	1000G_HIGH_COVERAGE	ss5558619799	Oct 13, 2022 (156)
70	SANFORD_IMAGENETICS	ss5642002758	Oct 13, 2022 (156)
71	TOMMO_GENOMICS	ss5720268256	Oct 13, 2022 (156)
72	YY_MCH	ss5808178981	Oct 13, 2022 (156)
73	EVA	ss5843338488	Oct 13, 2022 (156)
74	EVA	ss5855690427	Oct 13, 2022 (156)
75	EVA	ss5886978398	Oct 13, 2022 (156)
76	EVA	ss5971120512	Oct 13, 2022 (156)
77	EVA	ss5971120513	Oct 13, 2022 (156)
78	1000Genomes	NC_000006.11 - 165208199	Oct 12, 2018 (152)
79	1000Genomes_30x	NC_000006.12 - 164794710	Oct 13, 2022 (156)
80	The Avon Longitudinal Study of Parents and Children	NC_000006.11 - 165208199	Oct 12, 2018 (152)
81	Chileans	NC_000006.11 - 165208199	Apr 26, 2020 (154)
82	Genetic variation in the Estonian population	NC_000006.11 - 165208199	Oct 12, 2018 (152)
83	The Danish reference pan genome	NC_000006.11 - 165208199	Apr 26, 2020 (154)
84	gnomAD - Genomes	NC_000006.12 - 164794710	Apr 26, 2021 (155)
85	Genome of the Netherlands Release 5	NC_000006.11 - 165208199	Apr 26, 2020 (154)
86	HapMap	NC_000006.12 - 164794710	Apr 26, 2020 (154)
87	KOREAN population from KRGDB	NC_000006.11 - 165208199	Apr 26, 2020 (154)
88	Korean Genome Project	NC_000006.12 - 164794710	Apr 26, 2020 (154)
89	Northern Sweden	NC_000006.11 - 165208199	Jul 13, 2019 (153)
90	Ancient Sardinia genome-wide 1240k capture data generation and analysis	NC_000006.11 - 165208199	Apr 26, 2021 (155)
91	Qatari	NC_000006.11 - 165208199	Apr 26, 2020 (154)
92	SGDP_PRJ	NC_000006.11 - 165208199	Apr 26, 2020 (154)
93	Siberian	NC_000006.11 - 165208199	Apr 26, 2020 (154)
94	8.3KJPN	NC_000006.11 - 165208199	Apr 26, 2021 (155)
95	14KJPN	NC_000006.12 - 164794710	Oct 13, 2022 (156)
96	TopMed	NC_000006.12 - 164794710	Apr 26, 2021 (155)
97	UK 10K study - Twins	NC_000006.11 - 165208199	Oct 12, 2018 (152)
98	A Vietnamese Genetic Variation Database	NC_000006.11 - 165208199	Jul 13, 2019 (153)
99	ALFA	NC_000006.12 - 164794710	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)
rs58647635	Feb 27, 2009 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
20418492, ss3913241098	NC_000006.11:165208198:C:A	NC_000006.12:164794709:C:A	(self)
ss111284790, ss116812312, ss162970626, ss202733461, ss211964425, ss254795043, ss279119402, ss285547626, ss293783434, ss1593343550, ss1712919929	NC_000006.10:165128188:C:T	NC_000006.12:164794709:C:T	(self)
35190397, 19628964, 397666, 14034253, 8164711, 8735654, 20418492, 7492115, 494703, 9050326, 18263465, 4882768, 39028845, 19628964, 4368766, ss222816539, ss233783397, ss240777336, ss559693607, ss654036843, ss983767243, ss1074235392, ss1323282917, ss1430971453, ss1581999772, ss1617243324, ss1660237357, ss1804788562, ss1927008396, ss1970584853, ss2024172137, ss2152366414, ss2626576378, ss2708007121, ss2847961383, ss3000354862, ss3347346672, ss3668296005, ss3734207250, ss3765983366, ss3785687904, ss3791004803, ss3795884281, ss3830324197, ss3838647178, ss3866246485, ss3913241098, ss3985268776, ss5181059538, ss5370627617, ss5508796880, ss5642002758, ss5843338488, ss5971120512, ss5971120513	NC_000006.11:165208198:C:T	NC_000006.12:164794709:C:T	(self)
46145734, 248359711, 3305547, 16940666, 54105360, 567781535, 12757466877, ss2290477880, ss3025878580, ss3648524013, ss3718776482, ss3809148121, ss3844097572, ss3960562665, ss4730403977, ss5271238976, ss5468601401, ss5558619799, ss5720268256, ss5808178981, ss5855690427, ss5886978398	NC_000006.12:164794709:C:T	NC_000006.12:164794709:C:T	(self)
ss12793129	NT_007422.12:7495539:C:T	NC_000006.12:164794709:C:T	(self)
ss6489685, ss23676424, ss44710591, ss66162482, ss76206889, ss82097565, ss98560997, ss143119157, ss157871882, ss172811066	NT_025741.15:69377655:C:T	NC_000006.12:164794709: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 rs4709898

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

rs4709898