Name: rs6686621
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.

rs6686621

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:154321449 (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>A
Variation Type: SNV Single Nucleotide Variation
Frequency: A=0.133779 (35410/264690, TOPMED)
A=0.143597 (20124/140142, GnomAD)
A=0.15841 (4476/28256, 14KJPN) (+ 15 more)
A=0.13949 (2635/18890, ALFA)
A=0.15990 (2680/16760, 8.3KJPN)
A=0.1329 (851/6404, 1000G_30x)
A=0.1330 (666/5008, 1000G)
A=0.1453 (560/3854, ALSPAC)
A=0.1440 (534/3708, TWINSUK)
A=0.1239 (363/2930, KOREAN)
A=0.1119 (205/1832, Korea1K)
A=0.133 (133/998, GoNL)
A=0.182 (109/600, NorthernSweden)
A=0.125 (27/216, Qatari)
A=0.121 (26/214, Vietnamese)
T=0.43 (41/96, SGDP_PRJ)
A=0.17 (7/40, GENOME_DK)
T=0.33 (6/18, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: AQP10 : 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	18890	T=0.86051	A=0.13949
European	Sub	14286	T=0.85818	A=0.14182
African	Sub	2946	T=0.8530	A=0.1470
African Others	Sub	114	T=0.868	A=0.132
African American	Sub	2832	T=0.8524	A=0.1476
Asian	Sub	112	T=0.884	A=0.116
East Asian	Sub	86	T=0.86	A=0.14
Other Asian	Sub	26	T=0.96	A=0.04
Latin American 1	Sub	146	T=0.897	A=0.103
Latin American 2	Sub	610	T=0.913	A=0.087
South Asian	Sub	98	T=0.85	A=0.15
Other	Sub	692	T=0.884	A=0.116

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=0.866221	A=0.133779
gnomAD - Genomes	Global	Study-wide	140142	T=0.856403	A=0.143597
gnomAD - Genomes	European	Sub	75886	T=0.84618	A=0.15382
gnomAD - Genomes	African	Sub	41998	T=0.85695	A=0.14305
gnomAD - Genomes	American	Sub	13650	T=0.89011	A=0.10989
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	T=0.8902	A=0.1098
gnomAD - Genomes	East Asian	Sub	3134	T=0.9075	A=0.0925
gnomAD - Genomes	Other	Sub	2150	T=0.8660	A=0.1340
14KJPN	JAPANESE	Study-wide	28256	T=0.84159	A=0.15841
Allele Frequency Aggregator	Total	Global	18890	T=0.86051	A=0.13949
Allele Frequency Aggregator	European	Sub	14286	T=0.85818	A=0.14182
Allele Frequency Aggregator	African	Sub	2946	T=0.8530	A=0.1470
Allele Frequency Aggregator	Other	Sub	692	T=0.884	A=0.116
Allele Frequency Aggregator	Latin American 2	Sub	610	T=0.913	A=0.087
Allele Frequency Aggregator	Latin American 1	Sub	146	T=0.897	A=0.103
Allele Frequency Aggregator	Asian	Sub	112	T=0.884	A=0.116
Allele Frequency Aggregator	South Asian	Sub	98	T=0.85	A=0.15
8.3KJPN	JAPANESE	Study-wide	16760	T=0.84010	A=0.15990
1000Genomes_30x	Global	Study-wide	6404	T=0.8671	A=0.1329
1000Genomes_30x	African	Sub	1786	T=0.8371	A=0.1629
1000Genomes_30x	Europe	Sub	1266	T=0.8499	A=0.1501
1000Genomes_30x	South Asian	Sub	1202	T=0.8719	A=0.1281
1000Genomes_30x	East Asian	Sub	1170	T=0.9060	A=0.0940
1000Genomes_30x	American	Sub	980	T=0.892	A=0.108
1000Genomes	Global	Study-wide	5008	T=0.8670	A=0.1330
1000Genomes	African	Sub	1322	T=0.8336	A=0.1664
1000Genomes	East Asian	Sub	1008	T=0.9048	A=0.0952
1000Genomes	Europe	Sub	1006	T=0.8529	A=0.1471
1000Genomes	South Asian	Sub	978	T=0.870	A=0.130
1000Genomes	American	Sub	694	T=0.892	A=0.108
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.8547	A=0.1453
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.8560	A=0.1440
KOREAN population from KRGDB	KOREAN	Study-wide	2930	T=0.8761	A=0.1239
Korean Genome Project	KOREAN	Study-wide	1832	T=0.8881	A=0.1119
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.867	A=0.133
Northern Sweden	ACPOP	Study-wide	600	T=0.818	A=0.182
Qatari	Global	Study-wide	216	T=0.875	A=0.125
A Vietnamese Genetic Variation Database	Global	Study-wide	214	T=0.879	A=0.121
SGDP_PRJ	Global	Study-wide	96	T=0.43	A=0.57
The Danish reference pan genome	Danish	Study-wide	40	T=0.82	A=0.17
Siberian	Global	Study-wide	18	T=0.33	A=0.67

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.154321449T>A
GRCh37.p13 chr 1	NC_000001.10:g.154293925T>A

Gene: AQP10, aquaporin 10 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
AQP10 transcript	NM_080429.3:c.105+189T>A	N/A	Intron Variant
AQP10 transcript variant X1	XM_011510104.3:c.105+189T… XM_011510104.3:c.105+189T>A	N/A	Intron Variant
AQP10 transcript variant X2	XM_047433547.1:c.-33+189T… XM_047433547.1:c.-33+189T>A	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	T=	A
GRCh38.p14 chr 1	NC_000001.11:g.154321449=	NC_000001.11:g.154321449T>A
GRCh37.p13 chr 1	NC_000001.10:g.154293925=	NC_000001.10:g.154293925T>A
AQP10 transcript	NM_080429.2:c.105+189=	NM_080429.2:c.105+189T>A
AQP10 transcript	NM_080429.3:c.105+189=	NM_080429.3:c.105+189T>A
AQP10 transcript variant X1	XM_011510104.3:c.105+189=	XM_011510104.3:c.105+189T>A
AQP10 transcript variant X2	XM_047433547.1:c.-33+189=	XM_047433547.1:c.-33+189T>A

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#.

57 SubSNP, 18 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	BCM_SSAHASNP	ss9869853	Jul 11, 2003 (116)
2	SSAHASNP	ss20577155	Apr 05, 2004 (121)
3	ABI	ss41211022	Mar 14, 2006 (126)
4	HGSV	ss77643886	Dec 07, 2007 (129)
5	BCMHGSC_JDW	ss87823841	Mar 23, 2008 (129)
6	1000GENOMES	ss108597744	Jan 23, 2009 (130)
7	1000GENOMES	ss111151674	Jan 25, 2009 (130)
8	ENSEMBL	ss131695320	Dec 01, 2009 (131)
9	ENSEMBL	ss138082922	Dec 01, 2009 (131)
10	COMPLETE_GENOMICS	ss164115604	Jul 04, 2010 (132)
11	COMPLETE_GENOMICS	ss167131099	Jul 04, 2010 (132)
12	BCM-HGSC-SUB	ss205301783	Jul 04, 2010 (132)
13	1000GENOMES	ss218650536	Jul 14, 2010 (132)
14	1000GENOMES	ss230731323	Jul 14, 2010 (132)
15	1000GENOMES	ss238379324	Jul 15, 2010 (132)
16	GMI	ss276050518	May 04, 2012 (137)
17	PJP	ss290636687	May 09, 2011 (134)
18	TISHKOFF	ss554692179	Apr 25, 2013 (138)
19	SSMP	ss648412908	Apr 25, 2013 (138)
20	EVA-GONL	ss975680852	Aug 21, 2014 (142)
21	JMKIDD_LAB	ss1068268287	Aug 21, 2014 (142)
22	1000GENOMES	ss1292918728	Aug 21, 2014 (142)
23	EVA_GENOME_DK	ss1574390816	Apr 01, 2015 (144)
24	EVA_UK10K_ALSPAC	ss1601210382	Apr 01, 2015 (144)
25	EVA_UK10K_TWINSUK	ss1644204415	Apr 01, 2015 (144)
26	HAMMER_LAB	ss1795089769	Sep 08, 2015 (146)
27	WEILL_CORNELL_DGM	ss1918914709	Feb 12, 2016 (147)
28	JJLAB	ss2019972842	Sep 14, 2016 (149)
29	USC_VALOUEV	ss2147997224	Dec 20, 2016 (150)
30	GRF	ss2697970033	Nov 08, 2017 (151)
31	GNOMAD	ss2761295332	Nov 08, 2017 (151)
32	SWEGEN	ss2987749175	Nov 08, 2017 (151)
33	BIOINF_KMB_FNS_UNIBA	ss3023743506	Nov 08, 2017 (151)
34	CSHL	ss3343709680	Nov 08, 2017 (151)
35	URBANLAB	ss3646790797	Oct 11, 2018 (152)
36	EVA_DECODE	ss3687778490	Jul 12, 2019 (153)
37	ACPOP	ss3727484118	Jul 12, 2019 (153)
38	EVA	ss3746805972	Jul 12, 2019 (153)
39	KHV_HUMAN_GENOMES	ss3799807961	Jul 12, 2019 (153)
40	EVA	ss3826423133	Apr 25, 2020 (154)
41	SGDP_PRJ	ss3850003138	Apr 25, 2020 (154)
42	KRGDB	ss3895208536	Apr 25, 2020 (154)
43	KOGIC	ss3945646929	Apr 25, 2020 (154)
44	TOPMED	ss4468239404	Apr 25, 2021 (155)
45	TOMMO_GENOMICS	ss5146474345	Apr 25, 2021 (155)
46	1000G_HIGH_COVERAGE	ss5244286921	Oct 17, 2022 (156)
47	EVA	ss5322038819	Oct 17, 2022 (156)
48	HUGCELL_USP	ss5444880862	Oct 17, 2022 (156)
49	EVA	ss5506028751	Oct 17, 2022 (156)
50	1000G_HIGH_COVERAGE	ss5517612196	Oct 17, 2022 (156)
51	SANFORD_IMAGENETICS	ss5626588210	Oct 17, 2022 (156)
52	TOMMO_GENOMICS	ss5673667055	Oct 17, 2022 (156)
53	YY_MCH	ss5801258610	Oct 17, 2022 (156)
54	EVA	ss5832663071	Oct 17, 2022 (156)
55	EVA	ss5849108128	Oct 17, 2022 (156)
56	EVA	ss5910238708	Oct 17, 2022 (156)
57	EVA	ss5938381908	Oct 17, 2022 (156)
58	1000Genomes	NC_000001.10 - 154293925	Oct 11, 2018 (152)
59	1000Genomes_30x	NC_000001.11 - 154321449	Oct 17, 2022 (156)
60	The Avon Longitudinal Study of Parents and Children	NC_000001.10 - 154293925	Oct 11, 2018 (152)
61	The Danish reference pan genome	NC_000001.10 - 154293925	Apr 25, 2020 (154)
62	gnomAD - Genomes	NC_000001.11 - 154321449	Apr 25, 2021 (155)
63	Genome of the Netherlands Release 5	NC_000001.10 - 154293925	Apr 25, 2020 (154)
64	KOREAN population from KRGDB	NC_000001.10 - 154293925	Apr 25, 2020 (154)
65	Korean Genome Project	NC_000001.11 - 154321449	Apr 25, 2020 (154)
66	Northern Sweden	NC_000001.10 - 154293925	Jul 12, 2019 (153)
67	Qatari	NC_000001.10 - 154293925	Apr 25, 2020 (154)
68	SGDP_PRJ	NC_000001.10 - 154293925	Apr 25, 2020 (154)
69	Siberian	NC_000001.10 - 154293925	Apr 25, 2020 (154)
70	8.3KJPN	NC_000001.10 - 154293925	Apr 25, 2021 (155)
71	14KJPN	NC_000001.11 - 154321449	Oct 17, 2022 (156)
72	TopMed	NC_000001.11 - 154321449	Apr 25, 2021 (155)
73	UK 10K study - Twins	NC_000001.10 - 154293925	Oct 11, 2018 (152)
74	A Vietnamese Genetic Variation Database	NC_000001.10 - 154293925	Jul 12, 2019 (153)
75	ALFA	NC_000001.11 - 154321449	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).

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss77643886	NC_000001.8:151106997:T:A	NC_000001.11:154321448:T:A	(self)
ss87823841, ss108597744, ss111151674, ss164115604, ss167131099, ss205301783, ss276050518, ss290636687	NC_000001.9:152560548:T:A	NC_000001.11:154321448:T:A	(self)
3710510, 2017177, 1707957, 876618, 2385930, 768983, 956639, 2020118, 513578, 4443652, 2017177, 433612, ss218650536, ss230731323, ss238379324, ss554692179, ss648412908, ss975680852, ss1068268287, ss1292918728, ss1574390816, ss1601210382, ss1644204415, ss1795089769, ss1918914709, ss2019972842, ss2147997224, ss2697970033, ss2761295332, ss2987749175, ss3343709680, ss3727484118, ss3746805972, ss3826423133, ss3850003138, ss3895208536, ss5146474345, ss5322038819, ss5506028751, ss5626588210, ss5832663071, ss5938381908	NC_000001.10:154293924:T:A	NC_000001.11:154321448:T:A	(self)
5138131, 26998129, 2024930, 7504159, 31845739, 1220937856, ss3023743506, ss3646790797, ss3687778490, ss3799807961, ss3945646929, ss4468239404, ss5244286921, ss5444880862, ss5517612196, ss5673667055, ss5801258610, ss5849108128, ss5910238708	NC_000001.11:154321448:T:A	NC_000001.11:154321448:T:A	(self)
ss41211022, ss131695320, ss138082922	NT_004487.19:5782566:T:A	NC_000001.11:154321448:T:A	(self)
ss9869853	NT_004668.15:743756:T:A	NC_000001.11:154321448:T:A	(self)
ss20577155	NT_079484.1:743756:T:A	NC_000001.11:154321448:T:A	(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 rs6686621

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

rs6686621