Name: rs60429821
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.

rs60429821

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr10:119977360 (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 / G>T
Variation Type: SNV Single Nucleotide Variation
Frequency: A=0.077838 (20603/264690, TOPMED)
A=0.04953 (1573/31760, ALFA)
A=0.0517 (331/6404, 1000G_30x) (+ 10 more)
A=0.0495 (248/5008, 1000G)
A=0.0429 (192/4480, Estonian)
A=0.0082 (24/2922, KOREAN)
A=0.0071 (13/1832, Korea1K)
A=0.082 (82/998, GoNL)
A=0.100 (60/600, NorthernSweden)
A=0.032 (7/216, Qatari)
A=0.03 (1/40, GENOME_DK)
G=0.50 (14/28, SGDP_PRJ)
A=0.50 (14/28, SGDP_PRJ)

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	31760	G=0.95047	A=0.04953, T=0.00000
European	Sub	23686	G=0.95364	A=0.04636, T=0.00000
African	Sub	5176	G=0.9330	A=0.0670, T=0.0000
African Others	Sub	182	G=0.934	A=0.066, T=0.000
African American	Sub	4994	G=0.9329	A=0.0671, T=0.0000
Asian	Sub	130	G=1.000	A=0.000, T=0.000
East Asian	Sub	102	G=1.000	A=0.000, T=0.000
Other Asian	Sub	28	G=1.00	A=0.00, T=0.00
Latin American 1	Sub	154	G=0.994	A=0.006, T=0.000
Latin American 2	Sub	646	G=0.994	A=0.006, T=0.000
South Asian	Sub	108	G=0.991	A=0.009, T=0.000
Other	Sub	1860	G=0.9344	A=0.0656, T=0.0000

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=0.922162	A=0.077838
Allele Frequency Aggregator	Total	Global	31760	G=0.95047	A=0.04953, T=0.00000
Allele Frequency Aggregator	European	Sub	23686	G=0.95364	A=0.04636, T=0.00000
Allele Frequency Aggregator	African	Sub	5176	G=0.9330	A=0.0670, T=0.0000
Allele Frequency Aggregator	Other	Sub	1860	G=0.9344	A=0.0656, T=0.0000
Allele Frequency Aggregator	Latin American 2	Sub	646	G=0.994	A=0.006, T=0.000
Allele Frequency Aggregator	Latin American 1	Sub	154	G=0.994	A=0.006, T=0.000
Allele Frequency Aggregator	Asian	Sub	130	G=1.000	A=0.000, T=0.000
Allele Frequency Aggregator	South Asian	Sub	108	G=0.991	A=0.009, T=0.000
1000Genomes_30x	Global	Study-wide	6404	G=0.9483	A=0.0517
1000Genomes_30x	African	Sub	1786	G=0.8970	A=0.1030
1000Genomes_30x	Europe	Sub	1266	G=0.9455	A=0.0545
1000Genomes_30x	South Asian	Sub	1202	G=0.9784	A=0.0216
1000Genomes_30x	East Asian	Sub	1170	G=0.9966	A=0.0034
1000Genomes_30x	American	Sub	980	G=0.951	A=0.049
1000Genomes	Global	Study-wide	5008	G=0.9505	A=0.0495
1000Genomes	African	Sub	1322	G=0.8979	A=0.1021
1000Genomes	East Asian	Sub	1008	G=0.9960	A=0.0040
1000Genomes	Europe	Sub	1006	G=0.9463	A=0.0537
1000Genomes	South Asian	Sub	978	G=0.979	A=0.021
1000Genomes	American	Sub	694	G=0.951	A=0.049
Genetic variation in the Estonian population	Estonian	Study-wide	4480	G=0.9571	A=0.0429
KOREAN population from KRGDB	KOREAN	Study-wide	2922	G=0.9918	A=0.0082
Korean Genome Project	KOREAN	Study-wide	1832	G=0.9929	A=0.0071
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	G=0.918	A=0.082
Northern Sweden	ACPOP	Study-wide	600	G=0.900	A=0.100
Qatari	Global	Study-wide	216	G=0.968	A=0.032
The Danish reference pan genome	Danish	Study-wide	40	G=0.97	A=0.03
SGDP_PRJ	Global	Study-wide	28	G=0.50	A=0.50

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.119977360G>A
GRCh38.p14 chr 10	NC_000010.11:g.119977360G>T
GRCh37.p13 chr 10	NC_000010.10:g.121736872G>A
GRCh37.p13 chr 10	NC_000010.10:g.121736872G>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=	A	T
GRCh38.p14 chr 10	NC_000010.11:g.119977360=	NC_000010.11:g.119977360G>A	NC_000010.11:g.119977360G>T
GRCh37.p13 chr 10	NC_000010.10:g.121736872=	NC_000010.10:g.121736872G>A	NC_000010.10:g.121736872G>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#.

53 SubSNP, 22 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	HGSV	ss80994666	Dec 15, 2007 (129)
2	1000GENOMES	ss109801045	Jan 24, 2009 (130)
3	BUSHMAN	ss202097114	Jul 04, 2010 (132)
4	1000GENOMES	ss211053550	Jul 14, 2010 (132)
5	1000GENOMES	ss224976101	Jul 14, 2010 (132)
6	1000GENOMES	ss235358425	Jul 15, 2010 (132)
7	ILLUMINA	ss482118018	May 04, 2012 (137)
8	ILLUMINA	ss482489568	May 04, 2012 (137)
9	ILLUMINA	ss534507231	Sep 08, 2015 (146)
10	TISHKOFF	ss562251530	Apr 25, 2013 (138)
11	ILLUMINA	ss779954131	Sep 08, 2015 (146)
12	ILLUMINA	ss781655001	Sep 08, 2015 (146)
13	ILLUMINA	ss835432956	Sep 08, 2015 (146)
14	EVA-GONL	ss987990869	Aug 21, 2014 (142)
15	1000GENOMES	ss1339330860	Aug 21, 2014 (142)
16	EVA_GENOME_DK	ss1575394205	Apr 01, 2015 (144)
17	EVA_DECODE	ss1597669966	Apr 01, 2015 (144)
18	EVA_UK10K_ALSPAC	ss1625579607	Apr 01, 2015 (144)
19	EVA_UK10K_ALSPAC	ss1625579608	Apr 01, 2015 (144)
20	EVA_UK10K_TWINSUK	ss1668573640	Apr 01, 2015 (144)
21	EVA_UK10K_TWINSUK	ss1668573641	Apr 01, 2015 (144)
22	WEILL_CORNELL_DGM	ss1931348121	Feb 12, 2016 (147)
23	JJLAB	ss2026410341	Sep 14, 2016 (149)
24	HUMAN_LONGEVITY	ss2178631631	Dec 20, 2016 (150)
25	ILLUMINA	ss2632770614	Nov 08, 2017 (151)
26	GNOMAD	ss2894145282	Nov 08, 2017 (151)
27	SWEGEN	ss3007254804	Nov 08, 2017 (151)
28	CSHL	ss3349340846	Nov 08, 2017 (151)
29	ILLUMINA	ss3626549448	Oct 12, 2018 (152)
30	ILLUMINA	ss3630792368	Oct 12, 2018 (152)
31	ILLUMINA	ss3641704732	Oct 12, 2018 (152)
32	EGCUT_WGS	ss3674673602	Jul 13, 2019 (153)
33	EVA_DECODE	ss3690813013	Jul 13, 2019 (153)
34	ACPOP	ss3737736124	Jul 13, 2019 (153)
35	EVA	ss3748686295	Jul 13, 2019 (153)
36	KHV_HUMAN_GENOMES	ss3814043195	Jul 13, 2019 (153)
37	EVA	ss3832365681	Apr 26, 2020 (154)
38	SGDP_PRJ	ss3875193763	Apr 26, 2020 (154)
39	KRGDB	ss3923372537	Apr 26, 2020 (154)
40	KOGIC	ss3968806488	Apr 26, 2020 (154)
41	TOPMED	ss4868815269	Apr 26, 2021 (155)
42	TOMMO_GENOMICS	ss5199776005	Apr 26, 2021 (155)
43	TOMMO_GENOMICS	ss5199776006	Apr 26, 2021 (155)
44	1000G_HIGH_COVERAGE	ss5285701329	Oct 16, 2022 (156)
45	EVA	ss5396469893	Oct 16, 2022 (156)
46	HUGCELL_USP	ss5481100647	Oct 16, 2022 (156)
47	1000G_HIGH_COVERAGE	ss5580498357	Oct 16, 2022 (156)
48	SANFORD_IMAGENETICS	ss5650229396	Oct 16, 2022 (156)
49	TOMMO_GENOMICS	ss5746234639	Oct 16, 2022 (156)
50	TOMMO_GENOMICS	ss5746234640	Oct 16, 2022 (156)
51	EVA	ss5825049348	Oct 16, 2022 (156)
52	EVA	ss5880800446	Oct 16, 2022 (156)
53	EVA	ss5941535828	Oct 16, 2022 (156)
54	1000Genomes	NC_000010.10 - 121736872	Oct 12, 2018 (152)
55	1000Genomes_30x	NC_000010.11 - 119977360	Oct 16, 2022 (156)
56	The Avon Longitudinal Study of Parents and Children Submission ignored due to conflicting rows: Row 28767625 (NC_000010.10:121736871:G:G 3556/3854, NC_000010.10:121736871:G:A 298/3854) Row 28767626 (NC_000010.10:121736871:G:G 3853/3854, NC_000010.10:121736871:G:T 1/3854)	-	Oct 12, 2018 (152)
57	The Avon Longitudinal Study of Parents and Children Submission ignored due to conflicting rows: Row 28767625 (NC_000010.10:121736871:G:G 3556/3854, NC_000010.10:121736871:G:A 298/3854) Row 28767626 (NC_000010.10:121736871:G:G 3853/3854, NC_000010.10:121736871:G:T 1/3854)	-	Oct 12, 2018 (152)
58	Genetic variation in the Estonian population	NC_000010.10 - 121736872	Oct 12, 2018 (152)
59	The Danish reference pan genome	NC_000010.10 - 121736872	Apr 26, 2020 (154)
60	gnomAD - Genomes Submission ignored due to conflicting rows: Row 365908442 (NC_000010.11:119977359:G:A 10784/140156) Row 365908443 (NC_000010.11:119977359:G:T 4/140178)	-	Apr 26, 2021 (155)
61	gnomAD - Genomes Submission ignored due to conflicting rows: Row 365908442 (NC_000010.11:119977359:G:A 10784/140156) Row 365908443 (NC_000010.11:119977359:G:T 4/140178)	-	Apr 26, 2021 (155)
62	Genome of the Netherlands Release 5	NC_000010.10 - 121736872	Apr 26, 2020 (154)
63	KOREAN population from KRGDB	NC_000010.10 - 121736872	Apr 26, 2020 (154)
64	Korean Genome Project	NC_000010.11 - 119977360	Apr 26, 2020 (154)
65	Northern Sweden	NC_000010.10 - 121736872	Jul 13, 2019 (153)
66	Qatari	NC_000010.10 - 121736872	Apr 26, 2020 (154)
67	SGDP_PRJ	NC_000010.10 - 121736872	Apr 26, 2020 (154)
68	8.3KJPN Submission ignored due to conflicting rows: Row 57745312 (NC_000010.10:121736871:G:A 218/16760) Row 57745313 (NC_000010.10:121736871:G:T 2/16760)	-	Apr 26, 2021 (155)
69	8.3KJPN Submission ignored due to conflicting rows: Row 57745312 (NC_000010.10:121736871:G:A 218/16760) Row 57745313 (NC_000010.10:121736871:G:T 2/16760)	-	Apr 26, 2021 (155)
70	14KJPN Submission ignored due to conflicting rows: Row 80071743 (NC_000010.11:119977359:G:A 386/28258) Row 80071744 (NC_000010.11:119977359:G:T 3/28258)	-	Oct 16, 2022 (156)
71	14KJPN Submission ignored due to conflicting rows: Row 80071743 (NC_000010.11:119977359:G:A 386/28258) Row 80071744 (NC_000010.11:119977359:G:T 3/28258)	-	Oct 16, 2022 (156)
72	TopMed	NC_000010.11 - 119977360	Apr 26, 2021 (155)
73	UK 10K study - Twins Submission ignored due to conflicting rows: Row 28767625 (NC_000010.10:121736871:G:G 3385/3708, NC_000010.10:121736871:G:A 323/3708) Row 28767626 (NC_000010.10:121736871:G:G 3708/3708, NC_000010.10:121736871:G:T 0/3708)	-	Oct 12, 2018 (152)
74	UK 10K study - Twins Submission ignored due to conflicting rows: Row 28767625 (NC_000010.10:121736871:G:G 3385/3708, NC_000010.10:121736871:G:A 323/3708) Row 28767626 (NC_000010.10:121736871:G:G 3708/3708, NC_000010.10:121736871:G:T 0/3708)	-	Oct 12, 2018 (152)
75	ALFA	NC_000010.11 - 119977360	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
ss80994666	NC_000010.8:121726861:G:A	NC_000010.11:119977359:G:A	(self)
ss109801045, ss202097114, ss211053550, ss482489568, ss1597669966	NC_000010.9:121726861:G:A	NC_000010.11:119977359:G:A	(self)
51787618, 20411850, 2353243, 12820847, 30549931, 11020989, 13390051, 27210743, ss224976101, ss235358425, ss482118018, ss534507231, ss562251530, ss779954131, ss781655001, ss835432956, ss987990869, ss1339330860, ss1575394205, ss1625579607, ss1668573640, ss1931348121, ss2026410341, ss2632770614, ss2894145282, ss3007254804, ss3349340846, ss3626549448, ss3630792368, ss3641704732, ss3674673602, ss3737736124, ss3748686295, ss3832365681, ss3875193763, ss3923372537, ss5199776005, ss5396469893, ss5650229396, ss5825049348, ss5941535828	NC_000010.10:121736871:G:A	NC_000010.11:119977359:G:A	(self)
68024292, 25184489, 84360924, 7245244230, ss2178631631, ss3690813013, ss3814043195, ss3968806488, ss4868815269, ss5285701329, ss5481100647, ss5580498357, ss5746234639, ss5880800446	NC_000010.11:119977359:G:A	NC_000010.11:119977359:G:A	(self)
ss1625579608, ss1668573641, ss5199776006	NC_000010.10:121736871:G:T	NC_000010.11:119977359:G:T	(self)
7245244230, ss5746234640	NC_000010.11:119977359:G:T	NC_000010.11:119977359: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 rs60429821

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

rs60429821