Name: rs698702
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.

rs698702

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr19:47450680 (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: G>A / G>C
Variation Type: SNV Single Nucleotide Variation
Frequency: G=0.296819 (78565/264690, TOPMED)
G=0.16006 (4523/28258, 14KJPN)
G=0.15823 (2652/16760, 8.3KJPN) (+ 15 more)
G=0.2719 (2211/8132, ALFA)
G=0.3495 (2238/6404, 1000G_30x)
G=0.3399 (1702/5008, 1000G)
G=0.1437 (644/4480, Estonian)
G=0.1546 (596/3854, ALSPAC)
G=0.1532 (568/3708, TWINSUK)
G=0.2468 (723/2930, KOREAN)
G=0.2254 (413/1832, Korea1K)
G=0.147 (147/998, GoNL)
G=0.187 (112/600, NorthernSweden)
G=0.230 (111/482, SGDP_PRJ)
G=0.194 (42/216, Qatari)
G=0.278 (60/216, Vietnamese)
G=0.25 (13/52, Siberian)
G=0.12 (5/40, GENOME_DK)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: SLC8A2 : 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	8132	G=0.2719	A=0.7281, C=0.0000
European	Sub	6824	G=0.1681	A=0.8319, C=0.0000
African	Sub	984	G=0.938	A=0.062, C=0.000
African Others	Sub	60	G=0.95	A=0.05, C=0.00
African American	Sub	924	G=0.937	A=0.063, C=0.000
Asian	Sub	18	G=0.78	A=0.22, C=0.00
East Asian	Sub	8	G=0.8	A=0.2, C=0.0
Other Asian	Sub	10	G=0.8	A=0.2, C=0.0
Latin American 1	Sub	8	G=1.0	A=0.0, C=0.0
Latin American 2	Sub	18	G=1.00	A=0.00, C=0.00
South Asian	Sub	14	G=0.86	A=0.14, C=0.00
Other	Sub	266	G=0.335	A=0.665, C=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	G=0.296819	A=0.703181
14KJPN	JAPANESE	Study-wide	28258	G=0.16006	A=0.83994
8.3KJPN	JAPANESE	Study-wide	16760	G=0.15823	A=0.84177
Allele Frequency Aggregator	Total	Global	8132	G=0.2719	A=0.7281, C=0.0000
Allele Frequency Aggregator	European	Sub	6824	G=0.1681	A=0.8319, C=0.0000
Allele Frequency Aggregator	African	Sub	984	G=0.938	A=0.062, C=0.000
Allele Frequency Aggregator	Other	Sub	266	G=0.335	A=0.665, C=0.000
Allele Frequency Aggregator	Latin American 2	Sub	18	G=1.00	A=0.00, C=0.00
Allele Frequency Aggregator	Asian	Sub	18	G=0.78	A=0.22, C=0.00
Allele Frequency Aggregator	South Asian	Sub	14	G=0.86	A=0.14, C=0.00
Allele Frequency Aggregator	Latin American 1	Sub	8	G=1.0	A=0.0, C=0.0
1000Genomes_30x	Global	Study-wide	6404	G=0.3495	A=0.6505
1000Genomes_30x	African	Sub	1786	G=0.6226	A=0.3774
1000Genomes_30x	Europe	Sub	1266	G=0.1524	A=0.8476
1000Genomes_30x	South Asian	Sub	1202	G=0.3045	A=0.6955
1000Genomes_30x	East Asian	Sub	1170	G=0.2761	A=0.7239
1000Genomes_30x	American	Sub	980	G=0.249	A=0.751
1000Genomes	Global	Study-wide	5008	G=0.3399	A=0.6601
1000Genomes	African	Sub	1322	G=0.6157	A=0.3843
1000Genomes	East Asian	Sub	1008	G=0.2768	A=0.7232
1000Genomes	Europe	Sub	1006	G=0.1491	A=0.8509
1000Genomes	South Asian	Sub	978	G=0.292	A=0.708
1000Genomes	American	Sub	694	G=0.249	A=0.751
Genetic variation in the Estonian population	Estonian	Study-wide	4480	G=0.1437	A=0.8562
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.1546	A=0.8454
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.1532	A=0.8468
KOREAN population from KRGDB	KOREAN	Study-wide	2930	G=0.2468	A=0.7532
Korean Genome Project	KOREAN	Study-wide	1832	G=0.2254	A=0.7746
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	G=0.147	A=0.853
Northern Sweden	ACPOP	Study-wide	600	G=0.187	A=0.813
SGDP_PRJ	Global	Study-wide	482	G=0.230	A=0.770
Qatari	Global	Study-wide	216	G=0.194	A=0.806
A Vietnamese Genetic Variation Database	Global	Study-wide	216	G=0.278	A=0.722
Siberian	Global	Study-wide	52	G=0.25	A=0.75
The Danish reference pan genome	Danish	Study-wide	40	G=0.12	A=0.88

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 19	NC_000019.10:g.47450680G>A
GRCh38.p14 chr 19	NC_000019.10:g.47450680G>C
GRCh37.p13 chr 19	NC_000019.9:g.47953937G>A
GRCh37.p13 chr 19	NC_000019.9:g.47953937G>C

Gene: SLC8A2, solute carrier family 8 member A2 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
SLC8A2 transcript	NM_015063.3:c.1341-2449C>T	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	G=	A	C
GRCh38.p14 chr 19	NC_000019.10:g.47450680=	NC_000019.10:g.47450680G>A	NC_000019.10:g.47450680G>C
GRCh37.p13 chr 19	NC_000019.9:g.47953937=	NC_000019.9:g.47953937G>A	NC_000019.9:g.47953937G>C
SLC8A2 transcript	NM_015063.2:c.1341-2449=	NM_015063.2:c.1341-2449C>T	NM_015063.2:c.1341-2449C>G
SLC8A2 transcript	NM_015063.3:c.1341-2449=	NM_015063.3:c.1341-2449C>T	NM_015063.3:c.1341-2449C>G
SLC8A2 transcript variant X1	XM_005259172.1:c.1341-2449=	XM_005259172.1:c.1341-2449C>T	XM_005259172.1:c.1341-2449C>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#.

77 SubSNP, 20 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	KWOK	ss1135598	Oct 04, 2000 (86)
2	TSC-CSHL	ss1381833	Oct 04, 2000 (86)
3	SC_JCM	ss3452851	Sep 28, 2001 (100)
4	SC_JCM	ss3642810	Sep 28, 2001 (100)
5	CSHL-HAPMAP	ss16801076	Feb 27, 2004 (120)
6	SSAHASNP	ss21533229	Apr 05, 2004 (121)
7	BCMHGSC_JDW	ss90991213	Mar 24, 2008 (129)
8	HUMANGENOME_JCVI	ss96270577	Feb 06, 2009 (130)
9	BGI	ss103442393	Dec 01, 2009 (131)
10	1000GENOMES	ss111446261	Jan 25, 2009 (130)
11	1000GENOMES	ss115208849	Jan 25, 2009 (130)
12	ENSEMBL	ss137703471	Dec 01, 2009 (131)
13	ENSEMBL	ss144087071	Dec 01, 2009 (131)
14	GMI	ss155956130	Dec 01, 2009 (131)
15	COMPLETE_GENOMICS	ss168273344	Jul 04, 2010 (132)
16	COMPLETE_GENOMICS	ss169896560	Jul 04, 2010 (132)
17	COMPLETE_GENOMICS	ss171802215	Jul 04, 2010 (132)
18	BUSHMAN	ss203771106	Jul 04, 2010 (132)
19	BCM-HGSC-SUB	ss208408246	Jul 04, 2010 (132)
20	1000GENOMES	ss228164387	Jul 14, 2010 (132)
21	1000GENOMES	ss237695332	Jul 15, 2010 (132)
22	1000GENOMES	ss243897065	Jul 15, 2010 (132)
23	BL	ss255714885	May 09, 2011 (134)
24	GMI	ss283230628	May 04, 2012 (137)
25	GMI	ss287391039	Apr 25, 2013 (138)
26	TISHKOFF	ss566019146	Apr 25, 2013 (138)
27	SSMP	ss661885826	Apr 25, 2013 (138)
28	EVA-GONL	ss994358227	Aug 21, 2014 (142)
29	JMKIDD_LAB	ss1081943034	Aug 21, 2014 (142)
30	1000GENOMES	ss1363403476	Aug 21, 2014 (142)
31	DDI	ss1428418828	Apr 01, 2015 (144)
32	EVA_GENOME_DK	ss1578660782	Apr 01, 2015 (144)
33	EVA_UK10K_ALSPAC	ss1638079739	Apr 01, 2015 (144)
34	EVA_UK10K_TWINSUK	ss1681073772	Apr 01, 2015 (144)
35	EVA_DECODE	ss1698413539	Apr 01, 2015 (144)
36	HAMMER_LAB	ss1809334196	Sep 08, 2015 (146)
37	WEILL_CORNELL_DGM	ss1937856364	Feb 12, 2016 (147)
38	GENOMED	ss1968653656	Jul 19, 2016 (147)
39	JJLAB	ss2029704455	Sep 14, 2016 (149)
40	USC_VALOUEV	ss2158249959	Dec 20, 2016 (150)
41	HUMAN_LONGEVITY	ss2226170600	Dec 20, 2016 (150)
42	SYSTEMSBIOZJU	ss2629349370	Nov 08, 2017 (151)
43	GRF	ss2702862946	Nov 08, 2017 (151)
44	GNOMAD	ss2963559088	Nov 08, 2017 (151)
45	SWEGEN	ss3017574622	Nov 08, 2017 (151)
46	BIOINF_KMB_FNS_UNIBA	ss3028682482	Nov 08, 2017 (151)
47	CSHL	ss3352329539	Nov 08, 2017 (151)
48	URBANLAB	ss3650928866	Oct 12, 2018 (152)
49	EGCUT_WGS	ss3684317898	Jul 13, 2019 (153)
50	EVA_DECODE	ss3702886019	Jul 13, 2019 (153)
51	ACPOP	ss3743089662	Jul 13, 2019 (153)
52	EVA	ss3756134048	Jul 13, 2019 (153)
53	PACBIO	ss3788547121	Jul 13, 2019 (153)
54	PACBIO	ss3793454296	Jul 13, 2019 (153)
55	PACBIO	ss3798341186	Jul 13, 2019 (153)
56	KHV_HUMAN_GENOMES	ss3821381966	Jul 13, 2019 (153)
57	EVA	ss3835491163	Apr 27, 2020 (154)
58	EVA	ss3841368251	Apr 27, 2020 (154)
59	EVA	ss3846874457	Apr 27, 2020 (154)
60	SGDP_PRJ	ss3888346634	Apr 27, 2020 (154)
61	KRGDB	ss3938484649	Apr 27, 2020 (154)
62	KOGIC	ss3981484350	Apr 27, 2020 (154)
63	TOPMED	ss5076825875	Apr 26, 2021 (155)
64	TOMMO_GENOMICS	ss5228046639	Apr 26, 2021 (155)
65	1000G_HIGH_COVERAGE	ss5307469181	Oct 13, 2022 (156)
66	EVA	ss5435211045	Oct 13, 2022 (156)
67	HUGCELL_USP	ss5499954737	Oct 13, 2022 (156)
68	EVA	ss5512116639	Oct 13, 2022 (156)
69	1000G_HIGH_COVERAGE	ss5613294717	Oct 13, 2022 (156)
70	SANFORD_IMAGENETICS	ss5662513917	Oct 13, 2022 (156)
71	TOMMO_GENOMICS	ss5786775838	Oct 13, 2022 (156)
72	YY_MCH	ss5817653738	Oct 13, 2022 (156)
73	EVA	ss5840633747	Oct 13, 2022 (156)
74	EVA	ss5852311531	Oct 13, 2022 (156)
75	EVA	ss5928333753	Oct 13, 2022 (156)
76	EVA	ss5953923105	Oct 13, 2022 (156)
77	EVA	ss5981059473	Oct 13, 2022 (156)
78	1000Genomes	NC_000019.9 - 47953937	Oct 12, 2018 (152)
79	1000Genomes_30x	NC_000019.10 - 47450680	Oct 13, 2022 (156)
80	The Avon Longitudinal Study of Parents and Children	NC_000019.9 - 47953937	Oct 12, 2018 (152)
81	Genetic variation in the Estonian population	NC_000019.9 - 47953937	Oct 12, 2018 (152)
82	The Danish reference pan genome	NC_000019.9 - 47953937	Apr 27, 2020 (154)
83	gnomAD - Genomes Submission ignored due to conflicting rows: Row 541768934 (NC_000019.10:47450679:G:A 100202/139958) Row 541768935 (NC_000019.10:47450679:G:C 1/140030)	-	Apr 26, 2021 (155)
84	gnomAD - Genomes Submission ignored due to conflicting rows: Row 541768934 (NC_000019.10:47450679:G:A 100202/139958) Row 541768935 (NC_000019.10:47450679:G:C 1/140030)	-	Apr 26, 2021 (155)
85	Genome of the Netherlands Release 5	NC_000019.9 - 47953937	Apr 27, 2020 (154)
86	KOREAN population from KRGDB	NC_000019.9 - 47953937	Apr 27, 2020 (154)
87	Korean Genome Project	NC_000019.10 - 47450680	Apr 27, 2020 (154)
88	Northern Sweden	NC_000019.9 - 47953937	Jul 13, 2019 (153)
89	Qatari	NC_000019.9 - 47953937	Apr 27, 2020 (154)
90	SGDP_PRJ	NC_000019.9 - 47953937	Apr 27, 2020 (154)
91	Siberian	NC_000019.9 - 47953937	Apr 27, 2020 (154)
92	8.3KJPN	NC_000019.9 - 47953937	Apr 26, 2021 (155)
93	14KJPN	NC_000019.10 - 47450680	Oct 13, 2022 (156)
94	TopMed	NC_000019.10 - 47450680	Apr 26, 2021 (155)
95	UK 10K study - Twins	NC_000019.9 - 47953937	Oct 12, 2018 (152)
96	A Vietnamese Genetic Variation Database	NC_000019.9 - 47953937	Jul 13, 2019 (153)
97	ALFA	NC_000019.10 - 47450680	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).

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss90991213, ss111446261, ss115208849, ss168273344, ss169896560, ss171802215, ss203771106, ss208408246, ss255714885, ss283230628, ss287391039, ss1698413539	NC_000019.8:52645748:G:A	NC_000019.10:47450679:G:A	(self)
76818943, 42534740, 30056146, 4842501, 18947826, 45662043, 16374527, 19898286, 40363614, 10766313, 86015946, 42534740, 9391169, ss228164387, ss237695332, ss243897065, ss566019146, ss661885826, ss994358227, ss1081943034, ss1363403476, ss1428418828, ss1578660782, ss1638079739, ss1681073772, ss1809334196, ss1937856364, ss1968653656, ss2029704455, ss2158249959, ss2629349370, ss2702862946, ss2963559088, ss3017574622, ss3352329539, ss3684317898, ss3743089662, ss3756134048, ss3788547121, ss3793454296, ss3798341186, ss3835491163, ss3841368251, ss3888346634, ss3938484649, ss5228046639, ss5435211045, ss5512116639, ss5662513917, ss5840633747, ss5953923105, ss5981059473	NC_000019.9:47953936:G:A	NC_000019.10:47450679:G:A	(self)
100820652, 37862351, 120612942, 292371539, 4597461940, ss2226170600, ss3028682482, ss3650928866, ss3702886019, ss3821381966, ss3846874457, ss3981484350, ss5076825875, ss5307469181, ss5499954737, ss5613294717, ss5786775838, ss5817653738, ss5852311531, ss5928333753	NC_000019.10:47450679:G:A	NC_000019.10:47450679:G:A	(self)
ss16801076, ss21533229	NT_011109.15:20222126:G:A	NC_000019.10:47450679:G:A	(self)
ss1135598, ss1381833, ss3452851, ss3642810, ss96270577, ss103442393, ss137703471, ss144087071, ss155956130	NT_011109.16:20222154:G:A	NC_000019.10:47450679:G:A	(self)
ss2963559088	NC_000019.9:47953936:G:C	NC_000019.10:47450679:G:C	(self)
4597461940	NC_000019.10:47450679:G:C	NC_000019.10:47450679:G: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 rs698702

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

rs698702