Name: rs11964090
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.

rs11964090

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr6:41131426 (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>C
Variation Type: SNV Single Nucleotide Variation
Frequency: C=0.102728 (27191/264690, TOPMED)
C=0.101448 (14225/140220, GnomAD)
C=0.00605 (171/28258, 14KJPN) (+ 19 more)
C=0.11186 (2723/24344, ALFA)
C=0.00561 (94/16760, 8.3KJPN)
C=0.0843 (540/6404, 1000G_30x)
C=0.0867 (434/5008, 1000G)
C=0.1364 (611/4480, Estonian)
C=0.1090 (420/3854, ALSPAC)
C=0.1060 (393/3708, TWINSUK)
C=0.0021 (6/2922, KOREAN)
C=0.0920 (174/1892, HapMap)
C=0.0027 (5/1832, Korea1K)
C=0.113 (113/998, GoNL)
C=0.078 (47/600, NorthernSweden)
C=0.093 (20/216, Qatari)
C=0.019 (4/214, Vietnamese)
T=0.50 (38/76, SGDP_PRJ)
C=0.50 (38/76, SGDP_PRJ)
C=0.07 (3/40, GENOME_DK)
T=0.5 (5/10, Siberian)
C=0.5 (5/10, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: ADCY10P1 : Intron Variant
Publications: 1 citation
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: 20231103111315

Population	Group	Sample Size	Ref Allele	Alt Allele	Ref HMOZ	Alt HMOZ	HTRZ	HWEP
Total	Global	24344	T=0.88814	C=0.11186	0.788038	0.011748	0.200214	0
European	Sub	18120	T=0.88245	C=0.11755	0.778256	0.013355	0.208389	0
African	Sub	4114	T=0.9057	C=0.0943	0.818668	0.007292	0.17404	0
African Others	Sub	148	T=0.926	C=0.074	0.864865	0.013514	0.121622	1
African American	Sub	3966	T=0.9049	C=0.0951	0.816944	0.00706	0.175996	1
Asian	Sub	124	T=1.000	C=0.000	1.0	0.0	0.0	N/A
East Asian	Sub	96	T=1.00	C=0.00	1.0	0.0	0.0	N/A
Other Asian	Sub	28	T=1.00	C=0.00	1.0	0.0	0.0	N/A
Latin American 1	Sub	168	T=0.857	C=0.143	0.738095	0.02381	0.238095	0
Latin American 2	Sub	670	T=0.910	C=0.090	0.826866	0.00597	0.167164	0
South Asian	Sub	98	T=0.89	C=0.11	0.77551	0.0	0.22449	0
Other	Sub	1050	T=0.8952	C=0.1048	0.79619	0.005714	0.198095	1

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=0.897272	C=0.102728
gnomAD - Genomes	Global	Study-wide	140220	T=0.898552	C=0.101448
gnomAD - Genomes	European	Sub	75924	T=0.89243	C=0.10757
gnomAD - Genomes	African	Sub	42028	T=0.90944	C=0.09056
gnomAD - Genomes	American	Sub	13660	T=0.88836	C=0.11164
gnomAD - Genomes	Ashkenazi Jewish	Sub	3322	T=0.8570	C=0.1430
gnomAD - Genomes	East Asian	Sub	3132	T=0.9949	C=0.0051
gnomAD - Genomes	Other	Sub	2154	T=0.8904	C=0.1096
14KJPN	JAPANESE	Study-wide	28258	T=0.99395	C=0.00605
Allele Frequency Aggregator	Total	Global	24344	T=0.88814	C=0.11186
Allele Frequency Aggregator	European	Sub	18120	T=0.88245	C=0.11755
Allele Frequency Aggregator	African	Sub	4114	T=0.9057	C=0.0943
Allele Frequency Aggregator	Other	Sub	1050	T=0.8952	C=0.1048
Allele Frequency Aggregator	Latin American 2	Sub	670	T=0.910	C=0.090
Allele Frequency Aggregator	Latin American 1	Sub	168	T=0.857	C=0.143
Allele Frequency Aggregator	Asian	Sub	124	T=1.000	C=0.000
Allele Frequency Aggregator	South Asian	Sub	98	T=0.89	C=0.11
8.3KJPN	JAPANESE	Study-wide	16760	T=0.99439	C=0.00561
1000Genomes_30x	Global	Study-wide	6404	T=0.9157	C=0.0843
1000Genomes_30x	African	Sub	1786	T=0.9166	C=0.0834
1000Genomes_30x	Europe	Sub	1266	T=0.8673	C=0.1327
1000Genomes_30x	South Asian	Sub	1202	T=0.8977	C=0.1023
1000Genomes_30x	East Asian	Sub	1170	T=0.9923	C=0.0077
1000Genomes_30x	American	Sub	980	T=0.907	C=0.093
1000Genomes	Global	Study-wide	5008	T=0.9133	C=0.0867
1000Genomes	African	Sub	1322	T=0.9123	C=0.0877
1000Genomes	East Asian	Sub	1008	T=0.9911	C=0.0089
1000Genomes	Europe	Sub	1006	T=0.8638	C=0.1362
1000Genomes	South Asian	Sub	978	T=0.895	C=0.105
1000Genomes	American	Sub	694	T=0.901	C=0.099
Genetic variation in the Estonian population	Estonian	Study-wide	4480	T=0.8636	C=0.1364
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.8910	C=0.1090
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.8940	C=0.1060
KOREAN population from KRGDB	KOREAN	Study-wide	2922	T=0.9979	C=0.0021
HapMap	Global	Study-wide	1892	T=0.9080	C=0.0920
HapMap	American	Sub	770	T=0.909	C=0.091
HapMap	African	Sub	692	T=0.896	C=0.104
HapMap	Asian	Sub	254	T=0.992	C=0.008
HapMap	Europe	Sub	176	T=0.830	C=0.170
Korean Genome Project	KOREAN	Study-wide	1832	T=0.9973	C=0.0027
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.887	C=0.113
Northern Sweden	ACPOP	Study-wide	600	T=0.922	C=0.078
Qatari	Global	Study-wide	216	T=0.907	C=0.093
A Vietnamese Genetic Variation Database	Global	Study-wide	214	T=0.981	C=0.019
SGDP_PRJ	Global	Study-wide	76	T=0.50	C=0.50
The Danish reference pan genome	Danish	Study-wide	40	T=0.93	C=0.07
Siberian	Global	Study-wide	10	T=0.5	C=0.5

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.41131426T>C
GRCh37.p13 chr 6	NC_000006.11:g.41099165T>C

Gene: ADCY10P1, ADCY10 pseudogene 1 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
ADCY10P1 transcript	NR_026938.2: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	T=	C
GRCh38.p14 chr 6	NC_000006.12:g.41131426=	NC_000006.12:g.41131426T>C
GRCh37.p13 chr 6	NC_000006.11:g.41099165=	NC_000006.11:g.41099165T>C

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#.

58 SubSNP, 20 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	CSHL-HAPMAP	ss17884162	Feb 28, 2004 (120)
2	ABI	ss44761853	Mar 13, 2006 (126)
3	KRIBB_YJKIM	ss65848874	Nov 29, 2006 (127)
4	ILLUMINA	ss75032561	Dec 06, 2007 (129)
5	BCMHGSC_JDW	ss93448654	Mar 24, 2008 (129)
6	1000GENOMES	ss110010180	Jan 24, 2009 (130)
7	KRIBB_YJKIM	ss119735884	Dec 01, 2009 (131)
8	ENSEMBL	ss143862538	Dec 01, 2009 (131)
9	ILLUMINA	ss171754348	Jul 04, 2010 (132)
10	1000GENOMES	ss222354657	Jul 14, 2010 (132)
11	1000GENOMES	ss233444371	Jul 14, 2010 (132)
12	PJP	ss293844845	May 09, 2011 (134)
13	ILLUMINA	ss536741592	Sep 08, 2015 (146)
14	TISHKOFF	ss559162664	Apr 25, 2013 (138)
15	SSMP	ss653101094	Apr 25, 2013 (138)
16	EVA-GONL	ss982857146	Aug 21, 2014 (142)
17	JMKIDD_LAB	ss1073561608	Aug 21, 2014 (142)
18	1000GENOMES	ss1319844784	Aug 21, 2014 (142)
19	DDI	ss1430700044	Apr 01, 2015 (144)
20	EVA_GENOME_DK	ss1581644183	Apr 01, 2015 (144)
21	EVA_DECODE	ss1592392394	Apr 01, 2015 (144)
22	EVA_UK10K_ALSPAC	ss1615429933	Apr 01, 2015 (144)
23	EVA_UK10K_TWINSUK	ss1658423966	Apr 01, 2015 (144)
24	EVA_SVP	ss1712858374	Apr 01, 2015 (144)
25	WEILL_CORNELL_DGM	ss1926113731	Feb 12, 2016 (147)
26	JJLAB	ss2023695876	Sep 14, 2016 (149)
27	USC_VALOUEV	ss2151873675	Dec 20, 2016 (150)
28	HUMAN_LONGEVITY	ss2283492219	Dec 20, 2016 (150)
29	GNOMAD	ss2838190317	Nov 08, 2017 (151)
30	SWEGEN	ss2998949317	Nov 08, 2017 (151)
31	BIOINF_KMB_FNS_UNIBA	ss3025639766	Nov 08, 2017 (151)
32	CSHL	ss3346930019	Nov 08, 2017 (151)
33	ILLUMINA	ss3629532392	Oct 12, 2018 (152)
34	ILLUMINA	ss3638626803	Oct 12, 2018 (152)
35	ILLUMINA	ss3643568144	Oct 12, 2018 (152)
36	EGCUT_WGS	ss3666840894	Jul 13, 2019 (153)
37	EVA_DECODE	ss3717070454	Jul 13, 2019 (153)
38	ACPOP	ss3733442015	Jul 13, 2019 (153)
39	EVA	ss3764935560	Jul 13, 2019 (153)
40	KHV_HUMAN_GENOMES	ss3808082678	Jul 13, 2019 (153)
41	EVA	ss3829887633	Apr 26, 2020 (154)
42	EVA	ss3838420495	Apr 26, 2020 (154)
43	EVA	ss3843864823	Apr 26, 2020 (154)
44	SGDP_PRJ	ss3864433584	Apr 26, 2020 (154)
45	KRGDB	ss3911230646	Apr 26, 2020 (154)
46	KOGIC	ss3958887027	Apr 26, 2020 (154)
47	EVA	ss4017272080	Apr 26, 2021 (155)
48	TOPMED	ss4700542656	Apr 26, 2021 (155)
49	TOMMO_GENOMICS	ss5177181303	Apr 26, 2021 (155)
50	1000G_HIGH_COVERAGE	ss5268194125	Oct 13, 2022 (156)
51	EVA	ss5365167993	Oct 13, 2022 (156)
52	HUGCELL_USP	ss5465891878	Oct 13, 2022 (156)
53	1000G_HIGH_COVERAGE	ss5553965678	Oct 13, 2022 (156)
54	SANFORD_IMAGENETICS	ss5640258742	Oct 13, 2022 (156)
55	TOMMO_GENOMICS	ss5715132761	Oct 13, 2022 (156)
56	EVA	ss5842144547	Oct 13, 2022 (156)
57	EVA	ss5883529136	Oct 13, 2022 (156)
58	EVA	ss5968754354	Oct 13, 2022 (156)
59	1000Genomes	NC_000006.11 - 41099165	Oct 12, 2018 (152)
60	1000Genomes_30x	NC_000006.12 - 41131426	Oct 13, 2022 (156)
61	The Avon Longitudinal Study of Parents and Children	NC_000006.11 - 41099165	Oct 12, 2018 (152)
62	Genetic variation in the Estonian population	NC_000006.11 - 41099165	Oct 12, 2018 (152)
63	The Danish reference pan genome	NC_000006.11 - 41099165	Apr 26, 2020 (154)
64	gnomAD - Genomes	NC_000006.12 - 41131426	Apr 26, 2021 (155)
65	Genome of the Netherlands Release 5	NC_000006.11 - 41099165	Apr 26, 2020 (154)
66	HapMap	NC_000006.12 - 41131426	Apr 26, 2020 (154)
67	KOREAN population from KRGDB	NC_000006.11 - 41099165	Apr 26, 2020 (154)
68	Korean Genome Project	NC_000006.12 - 41131426	Apr 26, 2020 (154)
69	Northern Sweden	NC_000006.11 - 41099165	Jul 13, 2019 (153)
70	Qatari	NC_000006.11 - 41099165	Apr 26, 2020 (154)
71	SGDP_PRJ	NC_000006.11 - 41099165	Apr 26, 2020 (154)
72	Siberian	NC_000006.11 - 41099165	Apr 26, 2020 (154)
73	8.3KJPN	NC_000006.11 - 41099165	Apr 26, 2021 (155)
74	14KJPN	NC_000006.12 - 41131426	Oct 13, 2022 (156)
75	TopMed	NC_000006.12 - 41131426	Apr 26, 2021 (155)
76	UK 10K study - Twins	NC_000006.11 - 41099165	Oct 12, 2018 (152)
77	A Vietnamese Genetic Variation Database	NC_000006.11 - 41099165	Jul 13, 2019 (153)
78	ALFA	NC_000006.12 - 41131426	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
ss93448654, ss110010180, ss293844845, ss1592392394, ss1712858374, ss3643568144	NC_000006.10:41207142:T:C	NC_000006.12:41131425:T:C	(self)
31622931, 17635457, 12579142, 7809122, 7849021, 18408040, 6726880, 8155661, 16450564, 4390029, 35150610, 17635457, 3915663, ss222354657, ss233444371, ss536741592, ss559162664, ss653101094, ss982857146, ss1073561608, ss1319844784, ss1430700044, ss1581644183, ss1615429933, ss1658423966, ss1926113731, ss2023695876, ss2151873675, ss2838190317, ss2998949317, ss3346930019, ss3629532392, ss3638626803, ss3666840894, ss3733442015, ss3764935560, ss3829887633, ss3838420495, ss3864433584, ss3911230646, ss4017272080, ss5177181303, ss5365167993, ss5640258742, ss5842144547, ss5968754354	NC_000006.11:41099164:T:C	NC_000006.12:41131425:T:C	(self)
41491613, 223124265, 3117488, 15265028, 48969865, 537920214, 11745783142, ss2283492219, ss3025639766, ss3717070454, ss3808082678, ss3843864823, ss3958887027, ss4700542656, ss5268194125, ss5465891878, ss5553965678, ss5715132761, ss5883529136	NC_000006.12:41131425:T:C	NC_000006.12:41131425:T:C	(self)
ss17884162	NT_007592.13:31896291:T:C	NC_000006.12:41131425:T:C	(self)
ss44761853, ss65848874, ss75032561, ss119735884, ss143862538, ss171754348	NT_007592.15:41039164:T:C	NC_000006.12:41131425:T:C	(self)

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

1 citation for rs11964090

PMID	Title	Author	Year	Journal
19019460	No evidence for shared etiology in two demyelinative disorders, MS and PLOSL.	Sulonen AM et al.	2009	Journal of neuroimmunology

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

rs11964090