Name: rs6650172
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.

rs6650172

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr11:5112385 (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
Variation Type: SNV Single Nucleotide Variation
Frequency: A=0.380275 (100655/264690, TOPMED)
A=0.380769 (53179/139662, GnomAD)
A=0.45506 (12859/28258, 14KJPN) (+ 15 more)
A=0.37877 (7155/18890, ALFA)
A=0.45554 (7634/16758, 8.3KJPN)
A=0.3887 (2489/6404, 1000G_30x)
A=0.3810 (1908/5008, 1000G)
A=0.4042 (1811/4480, Estonian)
A=0.3726 (1436/3854, ALSPAC)
A=0.3805 (1411/3708, TWINSUK)
A=0.4915 (1440/2930, KOREAN)
A=0.357 (356/998, GoNL)
A=0.297 (178/600, NorthernSweden)
G=0.347 (116/334, SGDP_PRJ)
A=0.338 (73/216, Qatari)
A=0.435 (93/214, Vietnamese)
A=0.30 (12/40, GENOME_DK)
G=0.28 (9/32, 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	18890	G=0.62123	A=0.37877
European	Sub	14286	G=0.62530	A=0.37470
African	Sub	2946	G=0.5886	A=0.4114
African Others	Sub	114	G=0.570	A=0.430
African American	Sub	2832	G=0.5893	A=0.4107
Asian	Sub	112	G=0.607	A=0.393
East Asian	Sub	86	G=0.59	A=0.41
Other Asian	Sub	26	G=0.65	A=0.35
Latin American 1	Sub	146	G=0.637	A=0.363
Latin American 2	Sub	610	G=0.674	A=0.326
South Asian	Sub	98	G=0.69	A=0.31
Other	Sub	692	G=0.618	A=0.382

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=0.619725	A=0.380275
gnomAD - Genomes	Global	Study-wide	139662	G=0.619231	A=0.380769
gnomAD - Genomes	European	Sub	75640	G=0.63320	A=0.36680
gnomAD - Genomes	African	Sub	41886	G=0.58678	A=0.41322
gnomAD - Genomes	American	Sub	13590	G=0.64334	A=0.35666
gnomAD - Genomes	Ashkenazi Jewish	Sub	3310	G=0.6807	A=0.3193
gnomAD - Genomes	East Asian	Sub	3090	G=0.5414	A=0.4586
gnomAD - Genomes	Other	Sub	2146	G=0.6249	A=0.3751
14KJPN	JAPANESE	Study-wide	28258	G=0.54494	A=0.45506
Allele Frequency Aggregator	Total	Global	18890	G=0.62123	A=0.37877
Allele Frequency Aggregator	European	Sub	14286	G=0.62530	A=0.37470
Allele Frequency Aggregator	African	Sub	2946	G=0.5886	A=0.4114
Allele Frequency Aggregator	Other	Sub	692	G=0.618	A=0.382
Allele Frequency Aggregator	Latin American 2	Sub	610	G=0.674	A=0.326
Allele Frequency Aggregator	Latin American 1	Sub	146	G=0.637	A=0.363
Allele Frequency Aggregator	Asian	Sub	112	G=0.607	A=0.393
Allele Frequency Aggregator	South Asian	Sub	98	G=0.69	A=0.31
8.3KJPN	JAPANESE	Study-wide	16758	G=0.54446	A=0.45554
1000Genomes_30x	Global	Study-wide	6404	G=0.6113	A=0.3887
1000Genomes_30x	African	Sub	1786	G=0.5476	A=0.4524
1000Genomes_30x	Europe	Sub	1266	G=0.6295	A=0.3705
1000Genomes_30x	South Asian	Sub	1202	G=0.7521	A=0.2479
1000Genomes_30x	East Asian	Sub	1170	G=0.5120	A=0.4880
1000Genomes_30x	American	Sub	980	G=0.650	A=0.350
1000Genomes	Global	Study-wide	5008	G=0.6190	A=0.3810
1000Genomes	African	Sub	1322	G=0.5658	A=0.4342
1000Genomes	East Asian	Sub	1008	G=0.5208	A=0.4792
1000Genomes	Europe	Sub	1006	G=0.6392	A=0.3608
1000Genomes	South Asian	Sub	978	G=0.749	A=0.251
1000Genomes	American	Sub	694	G=0.650	A=0.350
Genetic variation in the Estonian population	Estonian	Study-wide	4480	G=0.5958	A=0.4042
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.6274	A=0.3726
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.6195	A=0.3805
KOREAN population from KRGDB	KOREAN	Study-wide	2930	G=0.5085	A=0.4915
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	G=0.643	A=0.357
Northern Sweden	ACPOP	Study-wide	600	G=0.703	A=0.297
SGDP_PRJ	Global	Study-wide	334	G=0.347	A=0.653
Qatari	Global	Study-wide	216	G=0.662	A=0.338
A Vietnamese Genetic Variation Database	Global	Study-wide	214	G=0.565	A=0.435
The Danish reference pan genome	Danish	Study-wide	40	G=0.70	A=0.30
Siberian	Global	Study-wide	32	G=0.28	A=0.72

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.5112385G>A
GRCh37.p13 chr 11	NC_000011.9:g.5133615G>A
GRCh38.p14 chr 11 fix patch HG2578_PATCH	NW_025791794.1:g.108706G>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	G=	A
GRCh38.p14 chr 11	NC_000011.10:g.5112385=	NC_000011.10:g.5112385G>A
GRCh37.p13 chr 11	NC_000011.9:g.5133615=	NC_000011.9:g.5133615G>A
GRCh38.p14 chr 11 fix patch HG2578_PATCH	NW_025791794.1:g.108706=	NW_025791794.1:g.108706G>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#.

70 SubSNP, 18 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_SNP	ss8820925	Jul 11, 2003 (116)
2	SC_SNP	ss16114792	Feb 27, 2004 (126)
3	SC_SNP	ss18052655	Feb 27, 2004 (126)
4	SC_SNP	ss18475435	Feb 27, 2004 (126)
5	SC_SNP	ss18702911	Feb 27, 2004 (126)
6	SC_SNP	ss18931387	Feb 27, 2004 (126)
7	CSHL-HAPMAP	ss19207727	Feb 27, 2004 (126)
8	SSAHASNP	ss20854233	Apr 05, 2004 (126)
9	BCMHGSC_JDW	ss88442483	Mar 23, 2008 (129)
10	1000GENOMES	ss109929028	Jan 24, 2009 (130)
11	COMPLETE_GENOMICS	ss167701027	Jul 04, 2010 (142)
12	COMPLETE_GENOMICS	ss168934772	Jul 04, 2010 (142)
13	COMPLETE_GENOMICS	ss170354234	Jul 04, 2010 (142)
14	BUSHMAN	ss202331877	Jul 04, 2010 (142)
15	1000GENOMES	ss225064340	Jul 14, 2010 (132)
16	1000GENOMES	ss235425571	Jul 15, 2010 (132)
17	1000GENOMES	ss242083642	Jul 15, 2010 (132)
18	BL	ss254845434	May 09, 2011 (134)
19	GMI	ss280864178	May 04, 2012 (137)
20	GMI	ss286305830	Apr 25, 2013 (138)
21	PJP	ss291103953	May 09, 2011 (134)
22	TISHKOFF	ss562353250	Apr 25, 2013 (138)
23	SSMP	ss657704618	Apr 25, 2013 (138)
24	EVA-GONL	ss988157793	Aug 21, 2014 (142)
25	JMKIDD_LAB	ss1077463943	Aug 21, 2014 (142)
26	1000GENOMES	ss1339935477	Aug 21, 2014 (142)
27	DDI	ss1426518692	Apr 01, 2015 (144)
28	EVA_GENOME_DK	ss1575491614	Apr 01, 2015 (144)
29	EVA_DECODE	ss1597834625	Apr 01, 2015 (144)
30	EVA_UK10K_ALSPAC	ss1625893758	Apr 01, 2015 (144)
31	EVA_UK10K_TWINSUK	ss1668887791	Apr 01, 2015 (144)
32	HAMMER_LAB	ss1806670869	Sep 08, 2015 (146)
33	WEILL_CORNELL_DGM	ss1931521902	Feb 12, 2016 (147)
34	GENOMED	ss1967278476	Jul 19, 2016 (147)
35	JJLAB	ss2026501069	Sep 14, 2016 (149)
36	USC_VALOUEV	ss2154787886	Dec 20, 2016 (150)
37	HUMAN_LONGEVITY	ss2179822548	Dec 20, 2016 (150)
38	SYSTEMSBIOZJU	ss2627719085	Nov 08, 2017 (151)
39	GRF	ss2699057354	Nov 08, 2017 (151)
40	GNOMAD	ss2895828534	Nov 08, 2017 (151)
41	SWEGEN	ss3007520991	Nov 08, 2017 (151)
42	BIOINF_KMB_FNS_UNIBA	ss3027042839	Nov 08, 2017 (151)
43	CSHL	ss3349429228	Nov 08, 2017 (151)
44	URBANLAB	ss3649520632	Oct 12, 2018 (152)
45	EGCUT_WGS	ss3674917103	Jul 13, 2019 (153)
46	EVA_DECODE	ss3691125077	Jul 13, 2019 (153)
47	ACPOP	ss3737877722	Jul 13, 2019 (153)
48	EVA	ss3748885716	Jul 13, 2019 (153)
49	PACBIO	ss3786851280	Jul 13, 2019 (153)
50	PACBIO	ss3792006580	Jul 13, 2019 (153)
51	PACBIO	ss3796888591	Jul 13, 2019 (153)
52	KHV_HUMAN_GENOMES	ss3814233845	Jul 13, 2019 (153)
53	EVA	ss3832451160	Apr 26, 2020 (154)
54	EVA	ss3839769988	Apr 26, 2020 (154)
55	EVA	ss3845245923	Apr 26, 2020 (154)
56	SGDP_PRJ	ss3875550132	Apr 26, 2020 (154)
57	KRGDB	ss3923773033	Apr 26, 2020 (154)
58	TOPMED	ss4873662009	Apr 26, 2021 (155)
59	TOMMO_GENOMICS	ss5200484495	Apr 26, 2021 (155)
60	1000G_HIGH_COVERAGE	ss5286246636	Oct 16, 2022 (156)
61	HUGCELL_USP	ss5481567338	Oct 16, 2022 (156)
62	EVA	ss5510234283	Oct 16, 2022 (156)
63	1000G_HIGH_COVERAGE	ss5581289556	Oct 16, 2022 (156)
64	SANFORD_IMAGENETICS	ss5650544740	Oct 16, 2022 (156)
65	TOMMO_GENOMICS	ss5747183155	Oct 16, 2022 (156)
66	YY_MCH	ss5812088030	Oct 16, 2022 (156)
67	EVA	ss5836198895	Oct 16, 2022 (156)
68	EVA	ss5849837385	Oct 16, 2022 (156)
69	EVA	ss5918648611	Oct 16, 2022 (156)
70	EVA	ss5941847876	Oct 16, 2022 (156)
71	1000Genomes	NC_000011.9 - 5133615	Oct 12, 2018 (152)
72	1000Genomes_30x	NC_000011.10 - 5112385	Oct 16, 2022 (156)
73	The Avon Longitudinal Study of Parents and Children	NC_000011.9 - 5133615	Oct 12, 2018 (152)
74	Genetic variation in the Estonian population	NC_000011.9 - 5133615	Oct 12, 2018 (152)
75	The Danish reference pan genome	NC_000011.9 - 5133615	Apr 26, 2020 (154)
76	gnomAD - Genomes	NC_000011.10 - 5112385	Apr 26, 2021 (155)
77	Genome of the Netherlands Release 5	NC_000011.9 - 5133615	Apr 26, 2020 (154)
78	KOREAN population from KRGDB	NC_000011.9 - 5133615	Apr 26, 2020 (154)
79	Northern Sweden	NC_000011.9 - 5133615	Jul 13, 2019 (153)
80	Qatari	NC_000011.9 - 5133615	Apr 26, 2020 (154)
81	SGDP_PRJ	NC_000011.9 - 5133615	Apr 26, 2020 (154)
82	Siberian	NC_000011.9 - 5133615	Apr 26, 2020 (154)
83	8.3KJPN	NC_000011.9 - 5133615	Apr 26, 2021 (155)
84	14KJPN	NC_000011.10 - 5112385	Oct 16, 2022 (156)
85	TopMed	NC_000011.10 - 5112385	Apr 26, 2021 (155)
86	UK 10K study - Twins	NC_000011.9 - 5133615	Oct 12, 2018 (152)
87	A Vietnamese Genetic Variation Database	NC_000011.9 - 5133615	Jul 13, 2019 (153)
88	ALFA	NC_000011.10 - 5112385	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)
rs10734478	Mar 10, 2006 (126)
rs113494178	Aug 21, 2014 (142)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss88442483, ss109929028, ss167701027, ss168934772, ss170354234, ss202331877, ss254845434, ss280864178, ss286305830, ss291103953, ss1597834625	NC_000011.8:5090190:G:A	NC_000011.10:5112384:G:A	(self)
52411816, 29110925, 20655351, 2421193, 12978081, 30950427, 11162587, 13563832, 27567112, 7304240, 58453802, 29110925, 6460812, ss225064340, ss235425571, ss242083642, ss562353250, ss657704618, ss988157793, ss1077463943, ss1339935477, ss1426518692, ss1575491614, ss1625893758, ss1668887791, ss1806670869, ss1931521902, ss1967278476, ss2026501069, ss2154787886, ss2627719085, ss2699057354, ss2895828534, ss3007520991, ss3349429228, ss3674917103, ss3737877722, ss3748885716, ss3786851280, ss3792006580, ss3796888591, ss3832451160, ss3839769988, ss3875550132, ss3923773033, ss5200484495, ss5510234283, ss5650544740, ss5836198895, ss5941847876	NC_000011.9:5133614:G:A	NC_000011.10:5112384:G:A	(self)
68815491, 370086081, 81020259, 89207665, 14335099504, ss2179822548, ss3027042839, ss3649520632, ss3691125077, ss3814233845, ss3845245923, ss4873662009, ss5286246636, ss5481567338, ss5581289556, ss5747183155, ss5812088030, ss5849837385, ss5918648611	NC_000011.10:5112384:G:A	NC_000011.10:5112384:G:A	(self)
ss16114792, ss18475435, ss18702911, ss18931387, ss19207727, ss20854233	NT_009237.16:3897554:G:A	NC_000011.10:5112384:G:A	(self)
ss8820925, ss18052655	NT_009237.18:5073614:G:A	NC_000011.10:5112384:G: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 rs6650172

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

rs6650172