Name: rs192339
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.

rs192339

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr11:43029719 (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=0.099218 (26262/264690, TOPMED)
C=0.096241 (13487/140138, GnomAD)
C=0.10379 (8054/77600, PAGE_STUDY) (+ 14 more)
C=0.08024 (1575/19628, ALFA)
C=0.0918 (588/6404, 1000G_30x)
C=0.0893 (447/5008, 1000G)
C=0.0364 (163/4480, Estonian)
C=0.0618 (238/3854, ALSPAC)
C=0.0564 (209/3708, TWINSUK)
C=0.069 (69/998, GoNL)
C=0.027 (16/600, NorthernSweden)
C=0.052 (16/308, HapMap)
C=0.106 (23/216, Qatari)
T=0.49 (36/74, SGDP_PRJ)
C=0.03 (1/40, GENOME_DK)
T=0.5 (2/4, Siberian)
C=0.5 (2/4, 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	19628	T=0.91976	C=0.08024
European	Sub	14364	T=0.94124	C=0.05876
African	Sub	3360	T=0.8185	C=0.1815
African Others	Sub	114	T=0.825	C=0.175
African American	Sub	3246	T=0.8182	C=0.1818
Asian	Sub	146	T=1.000	C=0.000
East Asian	Sub	120	T=1.000	C=0.000
Other Asian	Sub	26	T=1.00	C=0.00
Latin American 1	Sub	146	T=0.925	C=0.075
Latin American 2	Sub	610	T=0.952	C=0.048
South Asian	Sub	104	T=0.971	C=0.029
Other	Sub	898	T=0.913	C=0.087

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=0.900782	C=0.099218
gnomAD - Genomes	Global	Study-wide	140138	T=0.903759	C=0.096241
gnomAD - Genomes	European	Sub	75938	T=0.94202	C=0.05798
gnomAD - Genomes	African	Sub	41936	T=0.81822	C=0.18178
gnomAD - Genomes	American	Sub	13658	T=0.92722	C=0.07278
gnomAD - Genomes	Ashkenazi Jewish	Sub	3320	T=0.9166	C=0.0834
gnomAD - Genomes	East Asian	Sub	3132	T=0.9997	C=0.0003
gnomAD - Genomes	Other	Sub	2154	T=0.9123	C=0.0877
The PAGE Study	Global	Study-wide	77600	T=0.89621	C=0.10379
The PAGE Study	AfricanAmerican	Sub	31572	T=0.82722	C=0.17278
The PAGE Study	Mexican	Sub	10786	T=0.94456	C=0.05544
The PAGE Study	Asian	Sub	8318	T=0.9998	C=0.0002
The PAGE Study	PuertoRican	Sub	7868	T=0.9109	C=0.0891
The PAGE Study	NativeHawaiian	Sub	4534	T=0.9793	C=0.0207
The PAGE Study	Cuban	Sub	4214	T=0.9058	C=0.0942
The PAGE Study	Dominican	Sub	3778	T=0.8878	C=0.1122
The PAGE Study	CentralAmerican	Sub	2446	T=0.9391	C=0.0609
The PAGE Study	SouthAmerican	Sub	1976	T=0.9459	C=0.0541
The PAGE Study	NativeAmerican	Sub	1254	T=0.9179	C=0.0821
The PAGE Study	SouthAsian	Sub	854	T=0.972	C=0.028
Allele Frequency Aggregator	Total	Global	19628	T=0.91976	C=0.08024
Allele Frequency Aggregator	European	Sub	14364	T=0.94124	C=0.05876
Allele Frequency Aggregator	African	Sub	3360	T=0.8185	C=0.1815
Allele Frequency Aggregator	Other	Sub	898	T=0.913	C=0.087
Allele Frequency Aggregator	Latin American 2	Sub	610	T=0.952	C=0.048
Allele Frequency Aggregator	Latin American 1	Sub	146	T=0.925	C=0.075
Allele Frequency Aggregator	Asian	Sub	146	T=1.000	C=0.000
Allele Frequency Aggregator	South Asian	Sub	104	T=0.971	C=0.029
1000Genomes_30x	Global	Study-wide	6404	T=0.9082	C=0.0918
1000Genomes_30x	African	Sub	1786	T=0.7805	C=0.2195
1000Genomes_30x	Europe	Sub	1266	T=0.9100	C=0.0900
1000Genomes_30x	South Asian	Sub	1202	T=0.9825	C=0.0175
1000Genomes_30x	East Asian	Sub	1170	T=1.0000	C=0.0000
1000Genomes_30x	American	Sub	980	T=0.938	C=0.062
1000Genomes	Global	Study-wide	5008	T=0.9107	C=0.0893
1000Genomes	African	Sub	1322	T=0.7791	C=0.2209
1000Genomes	East Asian	Sub	1008	T=0.9990	C=0.0010
1000Genomes	Europe	Sub	1006	T=0.9076	C=0.0924
1000Genomes	South Asian	Sub	978	T=0.985	C=0.015
1000Genomes	American	Sub	694	T=0.934	C=0.066
Genetic variation in the Estonian population	Estonian	Study-wide	4480	T=0.9636	C=0.0364
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.9382	C=0.0618
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.9436	C=0.0564
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.931	C=0.069
Northern Sweden	ACPOP	Study-wide	600	T=0.973	C=0.027
HapMap	Global	Study-wide	308	T=0.948	C=0.052
HapMap	American	Sub	114	T=0.965	C=0.035
HapMap	African	Sub	106	T=0.887	C=0.113
HapMap	Asian	Sub	88	T=1.00	C=0.00
Qatari	Global	Study-wide	216	T=0.894	C=0.106
SGDP_PRJ	Global	Study-wide	74	T=0.49	C=0.51
The Danish reference pan genome	Danish	Study-wide	40	T=0.97	C=0.03
Siberian	Global	Study-wide	4	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 11	NC_000011.10:g.43029719T>C
GRCh37.p13 chr 11	NC_000011.9:g.43051269T>C

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 11	NC_000011.10:g.43029719=	NC_000011.10:g.43029719T>C
GRCh37.p13 chr 11	NC_000011.9:g.43051269=	NC_000011.9:g.43051269T>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#.

48 SubSNP, 16 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	KWOK	ss253549	Jul 12, 2000 (79)
2	SC_JCM	ss533734	Jul 16, 2000 (89)
3	KWOK	ss1067855	Oct 04, 2000 (86)
4	SC_JCM	ss3435666	Sep 28, 2001 (100)
5	COMPLETE_GENOMICS	ss169790845	Jul 04, 2010 (132)
6	BUSHMAN	ss202649581	Jul 04, 2010 (132)
7	1000GENOMES	ss211126137	Jul 14, 2010 (132)
8	1000GENOMES	ss225222185	Jul 14, 2010 (132)
9	1000GENOMES	ss235540542	Jul 15, 2010 (132)
10	GMI	ss286363985	Apr 25, 2013 (138)
11	TISHKOFF	ss562536293	Apr 25, 2013 (138)
12	EVA-GONL	ss988464814	Aug 21, 2014 (142)
13	JMKIDD_LAB	ss1077692745	Aug 21, 2014 (142)
14	1000GENOMES	ss1341048136	Aug 21, 2014 (142)
15	EVA_GENOME_DK	ss1575678071	Apr 01, 2015 (144)
16	EVA_DECODE	ss1598140750	Apr 01, 2015 (144)
17	EVA_UK10K_ALSPAC	ss1626484560	Apr 01, 2015 (144)
18	EVA_UK10K_TWINSUK	ss1669478593	Apr 01, 2015 (144)
19	HAMMER_LAB	ss1806801052	Sep 08, 2015 (146)
20	WEILL_CORNELL_DGM	ss1931823021	Feb 12, 2016 (147)
21	ILLUMINA	ss1959343592	Feb 12, 2016 (147)
22	USC_VALOUEV	ss2154949603	Dec 20, 2016 (150)
23	HUMAN_LONGEVITY	ss2182109062	Dec 20, 2016 (150)
24	GNOMAD	ss2898945047	Nov 08, 2017 (151)
25	SWEGEN	ss3007979127	Nov 08, 2017 (151)
26	ILLUMINA	ss3021329405	Nov 08, 2017 (151)
27	BIOINF_KMB_FNS_UNIBA	ss3027128931	Nov 08, 2017 (151)
28	CSHL	ss3349566777	Nov 08, 2017 (151)
29	ILLUMINA	ss3651692998	Oct 12, 2018 (152)
30	EGCUT_WGS	ss3675387302	Jul 13, 2019 (153)
31	EVA_DECODE	ss3691676097	Jul 13, 2019 (153)
32	ILLUMINA	ss3725235845	Jul 13, 2019 (153)
33	ACPOP	ss3738132854	Jul 13, 2019 (153)
34	EVA	ss3749230698	Jul 13, 2019 (153)
35	PAGE_CC	ss3771620664	Jul 13, 2019 (153)
36	KHV_HUMAN_GENOMES	ss3814580690	Jul 13, 2019 (153)
37	EVA	ss3832602978	Apr 26, 2020 (154)
38	SGDP_PRJ	ss3876137143	Apr 26, 2020 (154)
39	TOPMED	ss4883309262	Apr 26, 2021 (155)
40	1000G_HIGH_COVERAGE	ss5287212442	Oct 13, 2022 (156)
41	EVA	ss5399222524	Oct 13, 2022 (156)
42	HUGCELL_USP	ss5482434145	Oct 13, 2022 (156)
43	EVA	ss5510345263	Oct 13, 2022 (156)
44	1000G_HIGH_COVERAGE	ss5582770394	Oct 13, 2022 (156)
45	SANFORD_IMAGENETICS	ss5651110591	Oct 13, 2022 (156)
46	EVA	ss5836583710	Oct 13, 2022 (156)
47	EVA	ss5919762102	Oct 13, 2022 (156)
48	EVA	ss5942426695	Oct 13, 2022 (156)
49	1000Genomes	NC_000011.9 - 43051269	Oct 12, 2018 (152)
50	1000Genomes_30x	NC_000011.10 - 43029719	Oct 13, 2022 (156)
51	The Avon Longitudinal Study of Parents and Children	NC_000011.9 - 43051269	Oct 12, 2018 (152)
52	Genetic variation in the Estonian population	NC_000011.9 - 43051269	Oct 12, 2018 (152)
53	The Danish reference pan genome	NC_000011.9 - 43051269	Apr 26, 2020 (154)
54	gnomAD - Genomes	NC_000011.10 - 43029719	Apr 26, 2021 (155)
55	Genome of the Netherlands Release 5	NC_000011.9 - 43051269	Apr 26, 2020 (154)
56	HapMap	NC_000011.10 - 43029719	Apr 26, 2020 (154)
57	Northern Sweden	NC_000011.9 - 43051269	Jul 13, 2019 (153)
58	The PAGE Study	NC_000011.10 - 43029719	Jul 13, 2019 (153)
59	Qatari	NC_000011.9 - 43051269	Apr 26, 2020 (154)
60	SGDP_PRJ	NC_000011.9 - 43051269	Apr 26, 2020 (154)
61	Siberian	NC_000011.9 - 43051269	Apr 26, 2020 (154)
62	TopMed	NC_000011.10 - 43029719	Apr 26, 2021 (155)
63	UK 10K study - Twins	NC_000011.9 - 43051269	Oct 12, 2018 (152)
64	ALFA	NC_000011.10 - 43029719	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)
rs407987	Nov 09, 2000 (89)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss169790845, ss202649581, ss211126137, ss286363985, ss1598140750	NC_000011.8:43007844:T:C	NC_000011.10:43029718:T:C	(self)
53565305, 29759770, 21125550, 2545058, 13277688, 11417719, 13864951, 28154123, 7465957, 29759770, ss225222185, ss235540542, ss562536293, ss988464814, ss1077692745, ss1341048136, ss1575678071, ss1626484560, ss1669478593, ss1806801052, ss1931823021, ss1959343592, ss2154949603, ss2898945047, ss3007979127, ss3021329405, ss3349566777, ss3651692998, ss3675387302, ss3738132854, ss3749230698, ss3832602978, ss3876137143, ss5399222524, ss5510345263, ss5651110591, ss5836583710, ss5942426695	NC_000011.9:43051268:T:C	NC_000011.10:43029718:T:C	(self)
70296329, 378048367, 604457, 842133, 98854918, 5247431408, ss2182109062, ss3027128931, ss3691676097, ss3725235845, ss3771620664, ss3814580690, ss4883309262, ss5287212442, ss5482434145, ss5582770394, ss5919762102	NC_000011.10:43029718:T:C	NC_000011.10:43029718:T:C	(self)
ss253549, ss533734, ss1067855, ss3435666	NT_009237.18:42991268:T:C	NC_000011.10:43029718:T: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 rs192339

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

rs192339