Name: rs10410890
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.

rs10410890

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr19:41520247 (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=0.112018 (29650/264690, TOPMED)
T=0.112940 (15801/139906, GnomAD)
T=0.00149 (42/28258, 14KJPN) (+ 16 more)
T=0.09042 (1708/18890, ALFA)
T=0.00119 (20/16760, 8.3KJPN)
T=0.1043 (668/6404, 1000G_30x)
T=0.0990 (496/5008, 1000G)
T=0.0875 (392/4480, Estonian)
T=0.0418 (161/3854, ALSPAC)
T=0.0345 (128/3708, TWINSUK)
T=0.0027 (8/2922, KOREAN)
T=0.036 (36/998, GoNL)
T=0.062 (37/600, NorthernSweden)
T=0.113 (37/326, HapMap)
T=0.069 (15/216, Qatari)
G=0.47 (31/66, SGDP_PRJ)
T=0.03 (1/40, GENOME_DK)
G=0.5 (4/8, Siberian)
T=0.5 (4/8, 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=0.90958	T=0.09042
European	Sub	14286	G=0.94421	T=0.05579
African	Sub	2946	G=0.7251	T=0.2749
African Others	Sub	114	G=0.675	T=0.325
African American	Sub	2832	G=0.7270	T=0.2730
Asian	Sub	112	G=1.000	T=0.000
East Asian	Sub	86	G=1.00	T=0.00
Other Asian	Sub	26	G=1.00	T=0.00
Latin American 1	Sub	146	G=0.945	T=0.055
Latin American 2	Sub	610	G=0.966	T=0.034
South Asian	Sub	98	G=0.98	T=0.02
Other	Sub	692	G=0.899	T=0.101

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=0.887982	T=0.112018
gnomAD - Genomes	Global	Study-wide	139906	G=0.887060	T=0.112940
gnomAD - Genomes	European	Sub	75804	G=0.95349	T=0.04651
gnomAD - Genomes	African	Sub	41872	G=0.72593	T=0.27407
gnomAD - Genomes	American	Sub	13632	G=0.96090	T=0.03910
gnomAD - Genomes	Ashkenazi Jewish	Sub	3314	G=0.9653	T=0.0347
gnomAD - Genomes	East Asian	Sub	3130	G=0.9997	T=0.0003
gnomAD - Genomes	Other	Sub	2154	G=0.9304	T=0.0696
14KJPN	JAPANESE	Study-wide	28258	G=0.99851	T=0.00149
Allele Frequency Aggregator	Total	Global	18890	G=0.90958	T=0.09042
Allele Frequency Aggregator	European	Sub	14286	G=0.94421	T=0.05579
Allele Frequency Aggregator	African	Sub	2946	G=0.7251	T=0.2749
Allele Frequency Aggregator	Other	Sub	692	G=0.899	T=0.101
Allele Frequency Aggregator	Latin American 2	Sub	610	G=0.966	T=0.034
Allele Frequency Aggregator	Latin American 1	Sub	146	G=0.945	T=0.055
Allele Frequency Aggregator	Asian	Sub	112	G=1.000	T=0.000
Allele Frequency Aggregator	South Asian	Sub	98	G=0.98	T=0.02
8.3KJPN	JAPANESE	Study-wide	16760	G=0.99881	T=0.00119
1000Genomes_30x	Global	Study-wide	6404	G=0.8957	T=0.1043
1000Genomes_30x	African	Sub	1786	G=0.6825	T=0.3175
1000Genomes_30x	Europe	Sub	1266	G=0.9652	T=0.0348
1000Genomes_30x	South Asian	Sub	1202	G=0.9892	T=0.0108
1000Genomes_30x	East Asian	Sub	1170	G=1.0000	T=0.0000
1000Genomes_30x	American	Sub	980	G=0.955	T=0.045
1000Genomes	Global	Study-wide	5008	G=0.9010	T=0.0990
1000Genomes	African	Sub	1322	G=0.6831	T=0.3169
1000Genomes	East Asian	Sub	1008	G=1.0000	T=0.0000
1000Genomes	Europe	Sub	1006	G=0.9612	T=0.0388
1000Genomes	South Asian	Sub	978	G=0.989	T=0.011
1000Genomes	American	Sub	694	G=0.961	T=0.039
Genetic variation in the Estonian population	Estonian	Study-wide	4480	G=0.9125	T=0.0875
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.9582	T=0.0418
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.9655	T=0.0345
KOREAN population from KRGDB	KOREAN	Study-wide	2922	G=0.9973	T=0.0027
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	G=0.964	T=0.036
Northern Sweden	ACPOP	Study-wide	600	G=0.938	T=0.062
HapMap	Global	Study-wide	326	G=0.887	T=0.113
HapMap	American	Sub	120	G=0.983	T=0.017
HapMap	African	Sub	116	G=0.698	T=0.302
HapMap	Asian	Sub	90	G=1.00	T=0.00
Qatari	Global	Study-wide	216	G=0.931	T=0.069
SGDP_PRJ	Global	Study-wide	66	G=0.47	T=0.53
The Danish reference pan genome	Danish	Study-wide	40	G=0.97	T=0.03
Siberian	Global	Study-wide	8	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 19	NC_000019.10:g.41520247G>T
GRCh37.p13 chr 19 fix patch HG1350_HG959_PATCH	NW_004775434.1:g.89286G>T
PLEKHA3P1 pseudogene	NG_000949.3:g.1707C>A
GRCh38.p14 chr 19 alt locus HSCHR19_3_CTG3_1	NT_187620.1:g.170096C>A
GRCh37.p13 chr 19	NC_000019.9:g.42026607G>T

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 19	NC_000019.10:g.41520247=	NC_000019.10:g.41520247G>T
GRCh37.p13 chr 19 fix patch HG1350_HG959_PATCH	NW_004775434.1:g.89286=	NW_004775434.1:g.89286G>T
PLEKHA3P1 pseudogene	NG_000949.3:g.1707=	NG_000949.3:g.1707C>A
GRCh38.p14 chr 19 alt locus HSCHR19_3_CTG3_1	NT_187620.1:g.170096=	NT_187620.1:g.170096C>A
GRCh37.p13 chr 19	NC_000019.9:g.42026607=	NC_000019.9:g.42026607G>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#.

48 SubSNP, 18 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	BCM_SSAHASNP	ss14704985	Dec 05, 2003 (119)
2	HGSV	ss78696059	Dec 06, 2007 (129)
3	ILLUMINA-UK	ss117709798	Feb 14, 2009 (130)
4	COMPLETE_GENOMICS	ss169772807	Jul 04, 2010 (132)
5	BUSHMAN	ss203757983	Jul 04, 2010 (132)
6	1000GENOMES	ss211965575	Jul 14, 2010 (132)
7	1000GENOMES	ss228145813	Jul 14, 2010 (132)
8	1000GENOMES	ss237681772	Jul 15, 2010 (132)
9	TISHKOFF	ss565991488	Apr 25, 2013 (138)
10	EVA-GONL	ss994313040	Aug 21, 2014 (142)
11	JMKIDD_LAB	ss1081913027	Aug 21, 2014 (142)
12	1000GENOMES	ss1363218377	Aug 21, 2014 (142)
13	EVA_GENOME_DK	ss1578644878	Apr 09, 2015 (144)
14	EVA_UK10K_ALSPAC	ss1637994787	Apr 09, 2015 (144)
15	EVA_UK10K_TWINSUK	ss1680988820	Apr 09, 2015 (144)
16	HAMMER_LAB	ss1809313799	Sep 11, 2015 (146)
17	WEILL_CORNELL_DGM	ss1937806849	Feb 17, 2016 (147)
18	ILLUMINA	ss1959865844	Feb 17, 2016 (147)
19	JJLAB	ss2029682825	Sep 28, 2016 (149)
20	USC_VALOUEV	ss2158224109	Oct 12, 2018 (152)
21	HUMAN_LONGEVITY	ss2225859152	Dec 20, 2016 (150)
22	GNOMAD	ss2963022235	Oct 12, 2018 (152)
23	SWEGEN	ss3017495578	Oct 12, 2018 (152)
24	ILLUMINA	ss3021907625	Oct 12, 2018 (152)
25	BIOINF_KMB_FNS_UNIBA	ss3028672891	Nov 08, 2017 (151)
26	CSHL	ss3352309146	Oct 12, 2018 (152)
27	ILLUMINA	ss3652333607	Oct 12, 2018 (152)
28	EGCUT_WGS	ss3684257599	Jul 13, 2019 (153)
29	EVA_DECODE	ss3702794938	Jul 13, 2019 (153)
30	ACPOP	ss3743050818	Jul 13, 2019 (153)
31	EVA	ss3756080717	Jul 13, 2019 (153)
32	KHV_HUMAN_GENOMES	ss3821328528	Jul 13, 2019 (153)
33	EVA	ss3835468889	Apr 27, 2020 (154)
34	SGDP_PRJ	ss3888246712	Apr 27, 2020 (154)
35	KRGDB	ss3938364889	Apr 27, 2020 (154)
36	GNOMAD	ss4331464166	Apr 26, 2021 (155)
37	TOPMED	ss5075275972	Apr 26, 2021 (155)
38	TOMMO_GENOMICS	ss5227825054	Apr 26, 2021 (155)
39	1000G_HIGH_COVERAGE	ss5307297616	Oct 13, 2022 (156)
40	EVA	ss5434926339	Oct 13, 2022 (156)
41	HUGCELL_USP	ss5499814498	Oct 13, 2022 (156)
42	EVA	ss5512106470	Oct 13, 2022 (156)
43	1000G_HIGH_COVERAGE	ss5613049561	Oct 13, 2022 (156)
44	SANFORD_IMAGENETICS	ss5662420116	Oct 13, 2022 (156)
45	TOMMO_GENOMICS	ss5786480081	Oct 13, 2022 (156)
46	EVA	ss5840569071	Oct 13, 2022 (156)
47	EVA	ss5928156521	Oct 13, 2022 (156)
48	EVA	ss5953833031	Oct 13, 2022 (156)
49	1000Genomes	NC_000019.9 - 42026607	Oct 12, 2018 (152)
50	1000Genomes_30x	NC_000019.10 - 41520247	Oct 13, 2022 (156)
51	The Avon Longitudinal Study of Parents and Children	NC_000019.9 - 42026607	Oct 12, 2018 (152)
52	Genetic variation in the Estonian population	NC_000019.9 - 42026607	Oct 12, 2018 (152)
53	The Danish reference pan genome	NC_000019.9 - 42026607	Apr 27, 2020 (154)
54	gnomAD - Genomes	NC_000019.10 - 41520247	Apr 26, 2021 (155)
55	Genome of the Netherlands Release 5	NC_000019.9 - 42026607	Apr 27, 2020 (154)
56	HapMap	NC_000019.10 - 41520247	Apr 27, 2020 (154)
57	KOREAN population from KRGDB	NC_000019.9 - 42026607	Apr 27, 2020 (154)
58	Northern Sweden	NC_000019.9 - 42026607	Jul 13, 2019 (153)
59	Qatari	NC_000019.9 - 42026607	Apr 27, 2020 (154)
60	SGDP_PRJ	NC_000019.9 - 42026607	Apr 27, 2020 (154)
61	Siberian	NC_000019.9 - 42026607	Apr 27, 2020 (154)
62	8.3KJPN	NC_000019.9 - 42026607	Apr 26, 2021 (155)
63	14KJPN	NC_000019.10 - 41520247	Oct 13, 2022 (156)
64	TopMed	NC_000019.10 - 41520247	Apr 26, 2021 (155)
65	UK 10K study - Twins	NC_000019.9 - 42026607	Oct 12, 2018 (152)
66	ALFA	NC_000019.10 - 41520247	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
ss78696059, ss117709798, ss169772807, ss203757983, ss211965575	NC_000019.8:46718446:G:T	NC_000019.10:41520246:G:T	(self)
76627652, 42439779, 29995847, 4827146, 18905727, 45542283, 16335683, 19848771, 40263692, 10740463, 85794361, 42439779, ss228145813, ss237681772, ss565991488, ss994313040, ss1081913027, ss1363218377, ss1578644878, ss1637994787, ss1680988820, ss1809313799, ss1937806849, ss1959865844, ss2029682825, ss2158224109, ss2963022235, ss3017495578, ss3021907625, ss3352309146, ss3652333607, ss3684257599, ss3743050818, ss3756080717, ss3835468889, ss3888246712, ss3938364889, ss5227825054, ss5434926339, ss5512106470, ss5662420116, ss5840569071, ss5953833031	NC_000019.9:42026606:G:T	NC_000019.10:41520246:G:T	(self)
100575496, 540437831, 1698009, 120317185, 290821636, 7092530859, ss2225859152, ss3028672891, ss3702794938, ss3821328528, ss4331464166, ss5075275972, ss5307297616, ss5499814498, ss5613049561, ss5786480081, ss5928156521	NC_000019.10:41520246:G:T	NC_000019.10:41520246:G:T	(self)
ss14704985	NT_011109.15:14294824:G:T	NC_000019.10:41520246: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 rs10410890

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

rs10410890