Name: rs11804171
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.

rs11804171

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:788439 (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=0.132631 (18502/139500, GnomAD)
A=0.09881 (2791/28246, 14KJPN)
A=0.09839 (1649/16760, 8.3KJPN) (+ 11 more)
A=0.10617 (1734/16332, ALFA)
A=0.1377 (882/6404, 1000G_30x)
A=0.1346 (674/5008, 1000G)
A=0.0253 (74/2930, KOREAN)
A=0.035 (35/998, GoNL)
A=0.030 (18/600, NorthernSweden)
A=0.201 (63/314, HapMap)
A=0.153 (33/216, Qatari)
T=0.414 (48/116, SGDP_PRJ)
T=0.5 (3/6, Siberian)
A=0.5 (3/6, Siberian)

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	16332	T=0.89383	A=0.10617
European	Sub	12080	T=0.94462	A=0.05538
African	Sub	2816	T=0.6697	A=0.3303
African Others	Sub	108	T=0.593	A=0.407
African American	Sub	2708	T=0.6728	A=0.3272
Asian	Sub	108	T=0.954	A=0.046
East Asian	Sub	84	T=0.94	A=0.06
Other Asian	Sub	24	T=1.00	A=0.00
Latin American 1	Sub	146	T=0.836	A=0.164
Latin American 2	Sub	610	T=0.949	A=0.051
South Asian	Sub	94	T=0.95	A=0.05
Other	Sub	478	T=0.854	A=0.146

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
gnomAD - Genomes	Global	Study-wide	139500	T=0.867369	A=0.132631
gnomAD - Genomes	European	Sub	75614	T=0.95626	A=0.04374
gnomAD - Genomes	African	Sub	41730	T=0.67445	A=0.32555
gnomAD - Genomes	American	Sub	13596	T=0.93277	A=0.06723
gnomAD - Genomes	Ashkenazi Jewish	Sub	3308	T=0.9002	A=0.0998
gnomAD - Genomes	East Asian	Sub	3120	T=0.9651	A=0.0349
gnomAD - Genomes	Other	Sub	2132	T=0.8795	A=0.1205
14KJPN	JAPANESE	Study-wide	28246	T=0.90119	A=0.09881
8.3KJPN	JAPANESE	Study-wide	16760	T=0.90161	A=0.09839
Allele Frequency Aggregator	Total	Global	16332	T=0.89383	A=0.10617
Allele Frequency Aggregator	European	Sub	12080	T=0.94462	A=0.05538
Allele Frequency Aggregator	African	Sub	2816	T=0.6697	A=0.3303
Allele Frequency Aggregator	Latin American 2	Sub	610	T=0.949	A=0.051
Allele Frequency Aggregator	Other	Sub	478	T=0.854	A=0.146
Allele Frequency Aggregator	Latin American 1	Sub	146	T=0.836	A=0.164
Allele Frequency Aggregator	Asian	Sub	108	T=0.954	A=0.046
Allele Frequency Aggregator	South Asian	Sub	94	T=0.95	A=0.05
1000Genomes_30x	Global	Study-wide	6404	T=0.8623	A=0.1377
1000Genomes_30x	African	Sub	1786	T=0.6232	A=0.3768
1000Genomes_30x	Europe	Sub	1266	T=0.9502	A=0.0498
1000Genomes_30x	South Asian	Sub	1202	T=0.9567	A=0.0433
1000Genomes_30x	East Asian	Sub	1170	T=0.9658	A=0.0342
1000Genomes_30x	American	Sub	980	T=0.945	A=0.055
1000Genomes	Global	Study-wide	5008	T=0.8654	A=0.1346
1000Genomes	African	Sub	1322	T=0.6180	A=0.3820
1000Genomes	East Asian	Sub	1008	T=0.9623	A=0.0377
1000Genomes	Europe	Sub	1006	T=0.9523	A=0.0477
1000Genomes	South Asian	Sub	978	T=0.956	A=0.044
1000Genomes	American	Sub	694	T=0.942	A=0.058
KOREAN population from KRGDB	KOREAN	Study-wide	2930	T=0.9747	A=0.0253
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.965	A=0.035
Northern Sweden	ACPOP	Study-wide	600	T=0.970	A=0.030
HapMap	Global	Study-wide	314	T=0.799	A=0.201
HapMap	African	Sub	118	T=0.610	A=0.390
HapMap	American	Sub	108	T=0.963	A=0.037
HapMap	Asian	Sub	88	T=0.85	A=0.15
Qatari	Global	Study-wide	216	T=0.847	A=0.153
SGDP_PRJ	Global	Study-wide	116	T=0.414	A=0.586
Siberian	Global	Study-wide	6	T=0.5	A=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 1	NC_000001.11:g.788439T>A
GRCh37.p13 chr 1	NC_000001.10:g.723819T>A

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.788439=	NC_000001.11:g.788439T>A
GRCh37.p13 chr 1	NC_000001.10:g.723819=	NC_000001.10:g.723819T>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#.

35 SubSNP, 13 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	CSHL-HAPMAP	ss17344796	Feb 28, 2004 (120)
2	HGSV	ss84601599	Dec 15, 2007 (130)
3	BUSHMAN	ss197885306	Jul 04, 2010 (132)
4	1000GENOMES	ss210449079	Jul 14, 2010 (132)
5	1000GENOMES	ss218190346	Jul 14, 2010 (132)
6	1000GENOMES	ss230395409	Jul 14, 2010 (132)
7	1000GENOMES	ss238114943	Jul 15, 2010 (132)
8	SSMP	ss647515879	Apr 25, 2013 (138)
9	EVA-GONL	ss974769088	Aug 21, 2014 (142)
10	JMKIDD_LAB	ss1067612315	Aug 21, 2014 (142)
11	1000GENOMES	ss1289338091	Aug 21, 2014 (142)
12	HAMMER_LAB	ss1793705489	Sep 08, 2015 (146)
13	WEILL_CORNELL_DGM	ss1917959780	Feb 12, 2016 (147)
14	JJLAB	ss2019498275	Sep 14, 2016 (149)
15	USC_VALOUEV	ss2147483832	Dec 20, 2016 (150)
16	GRF	ss2697374048	Nov 08, 2017 (151)
17	GNOMAD	ss2750633519	Nov 08, 2017 (151)
18	SWEGEN	ss2986147805	Nov 08, 2017 (151)
19	CSHL	ss3343272202	Nov 08, 2017 (151)
20	ACPOP	ss3726716017	Jul 12, 2019 (153)
21	EVA	ss3745720727	Jul 12, 2019 (153)
22	KHV_HUMAN_GENOMES	ss3798743139	Jul 12, 2019 (153)
23	SGDP_PRJ	ss3847993910	Apr 25, 2020 (154)
24	KRGDB	ss3892833347	Apr 25, 2020 (154)
25	TOMMO_GENOMICS	ss5142049610	Apr 25, 2021 (155)
26	1000G_HIGH_COVERAGE	ss5240861535	Oct 12, 2022 (156)
27	EVA	ss5316180903	Oct 12, 2022 (156)
28	1000G_HIGH_COVERAGE	ss5512485865	Oct 12, 2022 (156)
29	SANFORD_IMAGENETICS	ss5624747956	Oct 12, 2022 (156)
30	TOMMO_GENOMICS	ss5666187953	Oct 12, 2022 (156)
31	YY_MCH	ss5800243166	Oct 12, 2022 (156)
32	EVA	ss5831417675	Oct 12, 2022 (156)
33	EVA	ss5848748807	Oct 12, 2022 (156)
34	EVA	ss5906704155	Oct 12, 2022 (156)
35	EVA	ss5936582169	Oct 12, 2022 (156)
36	1000Genomes	NC_000001.10 - 723819	Oct 11, 2018 (152)
37	1000Genomes_30x	NC_000001.11 - 788439	Oct 12, 2022 (156)
38	gnomAD - Genomes	NC_000001.11 - 788439	Apr 25, 2021 (155)
39	Genome of the Netherlands Release 5	NC_000001.10 - 723819	Apr 25, 2020 (154)
40	HapMap	NC_000001.11 - 788439	Apr 25, 2020 (154)
41	KOREAN population from KRGDB	NC_000001.10 - 723819	Apr 25, 2020 (154)
42	Northern Sweden	NC_000001.10 - 723819	Jul 12, 2019 (153)
43	Qatari	NC_000001.10 - 723819	Apr 25, 2020 (154)
44	SGDP_PRJ	NC_000001.10 - 723819	Apr 25, 2020 (154)
45	Siberian	NC_000001.10 - 723819	Apr 25, 2020 (154)
46	8.3KJPN	NC_000001.10 - 723819	Apr 25, 2021 (155)
47	14KJPN	NC_000001.11 - 788439	Oct 12, 2022 (156)
48	ALFA	NC_000001.11 - 788439	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).

Associated ID	History Updated (Build)
rs59714083	May 25, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss84601599	NC_000001.8:763681:T:A	NC_000001.11:788438:T:A	(self)
ss197885306, ss210449079	NC_000001.9:713681:T:A	NC_000001.11:788438:T:A	(self)
2767, 200, 10741, 882, 1710, 10890, 186, 18917, ss218190346, ss230395409, ss238114943, ss647515879, ss974769088, ss1067612315, ss1289338091, ss1793705489, ss1917959780, ss2019498275, ss2147483832, ss2697374048, ss2750633519, ss2986147805, ss3343272202, ss3726716017, ss3745720727, ss3847993910, ss3892833347, ss5142049610, ss5316180903, ss5624747956, ss5831417675, ss5936582169	NC_000001.10:723818:T:A	NC_000001.11:788438:T:A	(self)
11800, 54871, 29, 25057, 5061612805, ss3798743139, ss5240861535, ss5512485865, ss5666187953, ss5800243166, ss5848748807, ss5906704155	NC_000001.11:788438:T:A	NC_000001.11:788438:T:A	(self)
ss17344796	NT_034471.3:202450:T:A	NC_000001.11:788438: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 rs11804171

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

rs11804171