Name: rs10899952
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.

rs10899952

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr10:43931573 (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>T
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.064181 (16988/264690, TOPMED)
T=0.043660 (8687/198968, ALFA)
T=0.059720 (8374/140220, GnomAD) (+ 20 more)
T=0.06611 (1868/28258, 14KJPN)
T=0.06516 (1092/16760, 8.3KJPN)
T=0.0771 (494/6404, 1000G_30x)
T=0.0757 (379/5008, 1000G)
T=0.0308 (138/4480, Estonian)
T=0.0355 (137/3854, ALSPAC)
T=0.0367 (136/3708, TWINSUK)
T=0.0815 (238/2922, KOREAN)
T=0.0715 (149/2084, HGDP_Stanford)
T=0.0830 (157/1892, HapMap)
T=0.0977 (179/1832, Korea1K)
T=0.043 (43/998, GoNL)
T=0.052 (31/600, NorthernSweden)
T=0.069 (15/216, Qatari)
T=0.061 (13/214, Vietnamese)
G=0.48 (45/94, SGDP_PRJ)
T=0.03 (2/80, Ancient Sardinia)
T=0.03 (1/40, GENOME_DK)
G=0.5 (1/2, Siberian)
T=0.5 (1/2, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: LINC00841 : 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	198968	G=0.956340	T=0.043660
European	Sub	171732	G=0.961719	T=0.038281
African	Sub	7094	G=0.9091	T=0.0909
African Others	Sub	264	G=0.898	T=0.102
African American	Sub	6830	G=0.9095	T=0.0905
Asian	Sub	702	G=0.930	T=0.070
East Asian	Sub	556	G=0.923	T=0.077
Other Asian	Sub	146	G=0.959	T=0.041
Latin American 1	Sub	842	G=0.948	T=0.052
Latin American 2	Sub	6894	G=0.8940	T=0.1060
South Asian	Sub	5042	G=0.9419	T=0.0581
Other	Sub	6662	G=0.9473	T=0.0527

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=0.935819	T=0.064181
Allele Frequency Aggregator	Total	Global	198968	G=0.956340	T=0.043660
Allele Frequency Aggregator	European	Sub	171732	G=0.961719	T=0.038281
Allele Frequency Aggregator	African	Sub	7094	G=0.9091	T=0.0909
Allele Frequency Aggregator	Latin American 2	Sub	6894	G=0.8940	T=0.1060
Allele Frequency Aggregator	Other	Sub	6662	G=0.9473	T=0.0527
Allele Frequency Aggregator	South Asian	Sub	5042	G=0.9419	T=0.0581
Allele Frequency Aggregator	Latin American 1	Sub	842	G=0.948	T=0.052
Allele Frequency Aggregator	Asian	Sub	702	G=0.930	T=0.070
gnomAD - Genomes	Global	Study-wide	140220	G=0.940280	T=0.059720
gnomAD - Genomes	European	Sub	75946	G=0.95992	T=0.04008
gnomAD - Genomes	African	Sub	42010	G=0.90524	T=0.09476
gnomAD - Genomes	American	Sub	13656	G=0.93161	T=0.06839
gnomAD - Genomes	Ashkenazi Jewish	Sub	3322	G=0.9675	T=0.0325
gnomAD - Genomes	East Asian	Sub	3132	G=0.9400	T=0.0600
gnomAD - Genomes	Other	Sub	2154	G=0.9448	T=0.0552
14KJPN	JAPANESE	Study-wide	28258	G=0.93389	T=0.06611
8.3KJPN	JAPANESE	Study-wide	16760	G=0.93484	T=0.06516
1000Genomes_30x	Global	Study-wide	6404	G=0.9229	T=0.0771
1000Genomes_30x	African	Sub	1786	G=0.8824	T=0.1176
1000Genomes_30x	Europe	Sub	1266	G=0.9652	T=0.0348
1000Genomes_30x	South Asian	Sub	1202	G=0.9343	T=0.0657
1000Genomes_30x	East Asian	Sub	1170	G=0.9376	T=0.0624
1000Genomes_30x	American	Sub	980	G=0.910	T=0.090
1000Genomes	Global	Study-wide	5008	G=0.9243	T=0.0757
1000Genomes	African	Sub	1322	G=0.8858	T=0.1142
1000Genomes	East Asian	Sub	1008	G=0.9345	T=0.0655
1000Genomes	Europe	Sub	1006	G=0.9652	T=0.0348
1000Genomes	South Asian	Sub	978	G=0.937	T=0.063
1000Genomes	American	Sub	694	G=0.906	T=0.094
Genetic variation in the Estonian population	Estonian	Study-wide	4480	G=0.9692	T=0.0308
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.9645	T=0.0355
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.9633	T=0.0367
KOREAN population from KRGDB	KOREAN	Study-wide	2922	G=0.9185	T=0.0815
HGDP-CEPH-db Supplement 1	Global	Study-wide	2084	G=0.9285	T=0.0715
HGDP-CEPH-db Supplement 1	Est_Asia	Sub	470	G=0.898	T=0.102
HGDP-CEPH-db Supplement 1	Central_South_Asia	Sub	414	G=0.932	T=0.068
HGDP-CEPH-db Supplement 1	Middle_Est	Sub	350	G=0.969	T=0.031
HGDP-CEPH-db Supplement 1	Europe	Sub	320	G=0.956	T=0.044
HGDP-CEPH-db Supplement 1	Africa	Sub	242	G=0.893	T=0.107
HGDP-CEPH-db Supplement 1	America	Sub	216	G=0.921	T=0.079
HGDP-CEPH-db Supplement 1	Oceania	Sub	72	G=0.93	T=0.07
HapMap	Global	Study-wide	1892	G=0.9170	T=0.0830
HapMap	American	Sub	770	G=0.905	T=0.095
HapMap	African	Sub	692	G=0.910	T=0.090
HapMap	Asian	Sub	254	G=0.925	T=0.075
HapMap	Europe	Sub	176	G=0.983	T=0.017
Korean Genome Project	KOREAN	Study-wide	1832	G=0.9023	T=0.0977
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	G=0.957	T=0.043
Northern Sweden	ACPOP	Study-wide	600	G=0.948	T=0.052
Qatari	Global	Study-wide	216	G=0.931	T=0.069
A Vietnamese Genetic Variation Database	Global	Study-wide	214	G=0.939	T=0.061
SGDP_PRJ	Global	Study-wide	94	G=0.48	T=0.52
Ancient Sardinia genome-wide 1240k capture data generation and analysis	Global	Study-wide	80	G=0.97	T=0.03
The Danish reference pan genome	Danish	Study-wide	40	G=0.97	T=0.03
Siberian	Global	Study-wide	2	G=0.5	T=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 10	NC_000010.11:g.43931573G>T
GRCh37.p13 chr 10	NC_000010.10:g.44427021G>T

Gene: LINC00841, long intergenic non-protein coding RNA 841 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LINC00841 transcript variant 1	NR_033846.2:n.	N/A	Intron Variant
LINC00841 transcript variant 2	NR_136147.1:n.	N/A	Intron Variant
LINC00841 transcript variant 3	NR_136148.1:n.	N/A	Genic Downstream Transcript 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	G=	T
GRCh38.p14 chr 10	NC_000010.11:g.43931573=	NC_000010.11:g.43931573G>T
GRCh37.p13 chr 10	NC_000010.10:g.44427021=	NC_000010.10:g.44427021G>T

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#.

101 SubSNP, 22 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_SNP	ss15787323	Feb 27, 2004 (120)
2	SC_SNP	ss18629824	Feb 27, 2004 (120)
3	SC_SNP	ss18875315	Feb 27, 2004 (120)
4	PERLEGEN	ss24085482	Sep 20, 2004 (123)
5	ILLUMINA	ss66908789	Dec 01, 2006 (127)
6	ILLUMINA	ss67037615	Dec 01, 2006 (127)
7	ILLUMINA	ss68093707	Dec 12, 2006 (127)
8	ILLUMINA	ss70506350	May 26, 2008 (130)
9	ILLUMINA	ss71032992	May 17, 2007 (127)
10	ILLUMINA	ss75718468	Dec 05, 2007 (129)
11	KRIBB_YJKIM	ss85027175	Dec 15, 2007 (130)
12	ILLUMINA	ss152867924	Dec 01, 2009 (131)
13	ILLUMINA	ss159151515	Dec 01, 2009 (131)
14	ILLUMINA	ss159935934	Dec 01, 2009 (131)
15	ILLUMINA	ss170724350	Jul 04, 2010 (132)
16	COMPLETE_GENOMICS	ss174510571	Jul 04, 2010 (132)
17	BUSHMAN	ss201444893	Jul 04, 2010 (132)
18	1000GENOMES	ss210955317	Jul 14, 2010 (132)
19	1000GENOMES	ss224692097	Jul 14, 2010 (132)
20	1000GENOMES	ss235151069	Jul 15, 2010 (132)
21	1000GENOMES	ss241862335	Jul 15, 2010 (132)
22	GMI	ss280591482	May 04, 2012 (137)
23	ILLUMINA	ss410780452	Sep 17, 2011 (135)
24	ILLUMINA	ss479396304	May 04, 2012 (137)
25	ILLUMINA	ss479399549	May 04, 2012 (137)
26	ILLUMINA	ss479809791	Sep 08, 2015 (146)
27	ILLUMINA	ss484498148	May 04, 2012 (137)
28	ILLUMINA	ss536650603	Sep 08, 2015 (146)
29	TISHKOFF	ss561918570	Apr 25, 2013 (138)
30	SSMP	ss656634801	Apr 25, 2013 (138)
31	ILLUMINA	ss778745274	Sep 08, 2015 (146)
32	ILLUMINA	ss782695622	Sep 08, 2015 (146)
33	ILLUMINA	ss783663781	Sep 08, 2015 (146)
34	ILLUMINA	ss831946663	Sep 08, 2015 (146)
35	ILLUMINA	ss832664130	Jul 13, 2019 (153)
36	ILLUMINA	ss834204896	Sep 08, 2015 (146)
37	EVA-GONL	ss987429335	Aug 21, 2014 (142)
38	JMKIDD_LAB	ss1076941733	Aug 21, 2014 (142)
39	1000GENOMES	ss1337212181	Aug 21, 2014 (142)
40	EVA_GENOME_DK	ss1575075248	Apr 01, 2015 (144)
41	EVA_DECODE	ss1597094700	Apr 01, 2015 (144)
42	EVA_UK10K_ALSPAC	ss1624459906	Apr 01, 2015 (144)
43	EVA_UK10K_TWINSUK	ss1667453939	Apr 01, 2015 (144)
44	EVA_SVP	ss1713175023	Apr 01, 2015 (144)
45	ILLUMINA	ss1751968711	Sep 08, 2015 (146)
46	HAMMER_LAB	ss1806361874	Sep 08, 2015 (146)
47	WEILL_CORNELL_DGM	ss1930779382	Feb 12, 2016 (147)
48	GENOMED	ss1967112786	Jul 19, 2016 (147)
49	JJLAB	ss2026113847	Sep 14, 2016 (149)
50	USC_VALOUEV	ss2154386806	Dec 20, 2016 (150)
51	HUMAN_LONGEVITY	ss2174363716	Dec 20, 2016 (150)
52	SYSTEMSBIOZJU	ss2627526079	Nov 08, 2017 (151)
53	ILLUMINA	ss2632704295	Nov 08, 2017 (151)
54	GRF	ss2698622929	Nov 08, 2017 (151)
55	GNOMAD	ss2888106588	Nov 08, 2017 (151)
56	SWEGEN	ss3006370619	Nov 08, 2017 (151)
57	CSHL	ss3349089174	Nov 08, 2017 (151)
58	ILLUMINA	ss3626435141	Oct 12, 2018 (152)
59	ILLUMINA	ss3630730545	Oct 12, 2018 (152)
60	ILLUMINA	ss3632947253	Oct 12, 2018 (152)
61	ILLUMINA	ss3633644285	Oct 12, 2018 (152)
62	ILLUMINA	ss3634400831	Oct 12, 2018 (152)
63	ILLUMINA	ss3635336875	Oct 12, 2018 (152)
64	ILLUMINA	ss3636082601	Oct 12, 2018 (152)
65	ILLUMINA	ss3637087522	Oct 12, 2018 (152)
66	ILLUMINA	ss3637846851	Oct 12, 2018 (152)
67	ILLUMINA	ss3638939263	Oct 12, 2018 (152)
68	ILLUMINA	ss3639781099	Oct 12, 2018 (152)
69	ILLUMINA	ss3640108173	Oct 12, 2018 (152)
70	ILLUMINA	ss3642850520	Oct 12, 2018 (152)
71	ILLUMINA	ss3643833862	Oct 12, 2018 (152)
72	EGCUT_WGS	ss3673810056	Jul 13, 2019 (153)
73	EVA_DECODE	ss3689768591	Jul 13, 2019 (153)
74	ACPOP	ss3737270207	Jul 13, 2019 (153)
75	ILLUMINA	ss3744701735	Jul 13, 2019 (153)
76	EVA	ss3748033887	Jul 13, 2019 (153)
77	ILLUMINA	ss3772202326	Jul 13, 2019 (153)
78	KHV_HUMAN_GENOMES	ss3813405822	Jul 13, 2019 (153)
79	EVA	ss3832092183	Apr 26, 2020 (154)
80	HGDP	ss3847383793	Apr 26, 2020 (154)
81	SGDP_PRJ	ss3874052413	Apr 26, 2020 (154)
82	KRGDB	ss3922117312	Apr 26, 2020 (154)
83	KOGIC	ss3967765394	Apr 26, 2020 (154)
84	EVA	ss3985471852	Apr 26, 2021 (155)
85	EVA	ss4017482608	Apr 26, 2021 (155)
86	TOPMED	ss4850436252	Apr 26, 2021 (155)
87	TOMMO_GENOMICS	ss5197354835	Apr 26, 2021 (155)
88	1000G_HIGH_COVERAGE	ss5283818733	Oct 16, 2022 (156)
89	EVA	ss5315468826	Oct 16, 2022 (156)
90	EVA	ss5393078706	Oct 16, 2022 (156)
91	HUGCELL_USP	ss5479457798	Oct 16, 2022 (156)
92	EVA	ss5509991183	Oct 16, 2022 (156)
93	1000G_HIGH_COVERAGE	ss5577642005	Oct 16, 2022 (156)
94	SANFORD_IMAGENETICS	ss5649160483	Oct 16, 2022 (156)
95	TOMMO_GENOMICS	ss5743096468	Oct 16, 2022 (156)
96	EVA	ss5799810724	Oct 16, 2022 (156)
97	YY_MCH	ss5811471261	Oct 16, 2022 (156)
98	EVA	ss5824312361	Oct 16, 2022 (156)
99	EVA	ss5849540423	Oct 16, 2022 (156)
100	EVA	ss5878686840	Oct 16, 2022 (156)
101	EVA	ss5940439435	Oct 16, 2022 (156)
102	1000Genomes	NC_000010.10 - 44427021	Oct 12, 2018 (152)
103	1000Genomes_30x	NC_000010.11 - 43931573	Oct 16, 2022 (156)
104	The Avon Longitudinal Study of Parents and Children	NC_000010.10 - 44427021	Oct 12, 2018 (152)
105	Genetic variation in the Estonian population	NC_000010.10 - 44427021	Oct 12, 2018 (152)
106	The Danish reference pan genome	NC_000010.10 - 44427021	Apr 26, 2020 (154)
107	gnomAD - Genomes	NC_000010.11 - 43931573	Apr 26, 2021 (155)
108	Genome of the Netherlands Release 5	NC_000010.10 - 44427021	Apr 26, 2020 (154)
109	HGDP-CEPH-db Supplement 1	NC_000010.9 - 43747027	Apr 26, 2020 (154)
110	HapMap	NC_000010.11 - 43931573	Apr 26, 2020 (154)
111	KOREAN population from KRGDB	NC_000010.10 - 44427021	Apr 26, 2020 (154)
112	Korean Genome Project	NC_000010.11 - 43931573	Apr 26, 2020 (154)
113	Northern Sweden	NC_000010.10 - 44427021	Jul 13, 2019 (153)
114	Ancient Sardinia genome-wide 1240k capture data generation and analysis	NC_000010.10 - 44427021	Apr 26, 2021 (155)
115	Qatari	NC_000010.10 - 44427021	Apr 26, 2020 (154)
116	SGDP_PRJ	NC_000010.10 - 44427021	Apr 26, 2020 (154)
117	Siberian	NC_000010.10 - 44427021	Apr 26, 2020 (154)
118	8.3KJPN	NC_000010.10 - 44427021	Apr 26, 2021 (155)
119	14KJPN	NC_000010.11 - 43931573	Oct 16, 2022 (156)
120	TopMed	NC_000010.11 - 43931573	Apr 26, 2021 (155)
121	UK 10K study - Twins	NC_000010.10 - 44427021	Oct 12, 2018 (152)
122	A Vietnamese Genetic Variation Database	NC_000010.10 - 44427021	Jul 13, 2019 (153)
123	ALFA	NC_000010.11 - 43931573	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)
rs60662387	May 26, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss3638939263, ss3639781099, ss3643833862	NC_000010.8:43747026:G:T	NC_000010.11:43931572:G:T	(self)
61685, ss174510571, ss201444893, ss210955317, ss280591482, ss479396304, ss1597094700, ss1713175023, ss3642850520, ss3847383793	NC_000010.9:43747026:G:T	NC_000010.11:43931572:G:T	(self)
49591693, 27536592, 19548304, 2130768, 12275690, 29294706, 10555072, 697779, 12821312, 26069393, 6903160, 55324142, 27536592, 6111621, ss224692097, ss235151069, ss241862335, ss479399549, ss479809791, ss484498148, ss536650603, ss561918570, ss656634801, ss778745274, ss782695622, ss783663781, ss831946663, ss832664130, ss834204896, ss987429335, ss1076941733, ss1337212181, ss1575075248, ss1624459906, ss1667453939, ss1751968711, ss1806361874, ss1930779382, ss1967112786, ss2026113847, ss2154386806, ss2627526079, ss2632704295, ss2698622929, ss2888106588, ss3006370619, ss3349089174, ss3626435141, ss3630730545, ss3632947253, ss3633644285, ss3634400831, ss3635336875, ss3636082601, ss3637087522, ss3637846851, ss3640108173, ss3673810056, ss3737270207, ss3744701735, ss3748033887, ss3772202326, ss3832092183, ss3874052413, ss3922117312, ss3985471852, ss4017482608, ss5197354835, ss5315468826, ss5393078706, ss5509991183, ss5649160483, ss5799810724, ss5824312361, ss5940439435	NC_000010.10:44427020:G:T	NC_000010.11:43931572:G:T	(self)
65167940, 350477249, 388563, 24143395, 76933572, 65981907, 14989137944, ss2174363716, ss3689768591, ss3813405822, ss3967765394, ss4850436252, ss5283818733, ss5479457798, ss5577642005, ss5743096468, ss5811471261, ss5849540423, ss5878686840	NC_000010.11:43931572:G:T	NC_000010.11:43931572:G:T	(self)
ss15787323, ss18629824, ss18875315	NT_033985.6:1830333:G:T	NC_000010.11:43931572:G:T	(self)
ss24085482, ss66908789, ss67037615, ss68093707, ss70506350, ss71032992, ss75718468, ss85027175, ss152867924, ss159151515, ss159935934, ss170724350, ss410780452	NT_033985.7:2072085:G:T	NC_000010.11:43931572:G:T	(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 rs10899952

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.

Choose placement

dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs10899952