Name: rs62323606
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.

rs62323606

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr4:99109578 (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: A>G / A>T
Variation Type: SNV Single Nucleotide Variation
Frequency: G=0.119581 (31652/264690, TOPMED)
G=0.108770 (15243/140140, GnomAD)
A=0.27267 (7705/28258, 14KJPN) (+ 18 more)
G=0.11646 (2200/18890, ALFA)
A=0.27136 (4548/16760, 8.3KJPN)
G=0.2295 (1470/6404, 1000G_30x)
G=0.2478 (1241/5008, 1000G)
G=0.1141 (511/4480, Estonian)
G=0.1373 (529/3854, ALSPAC)
G=0.1294 (480/3708, TWINSUK)
A=0.3137 (919/2930, KOREAN)
A=0.2991 (548/1832, Korea1K)
G=0.127 (127/998, GoNL)
G=0.088 (53/600, NorthernSweden)
G=0.006 (3/534, MGP)
G=0.134 (29/216, Qatari)
A=0.204 (44/216, Vietnamese)
A=0.370 (77/208, SGDP_PRJ)
G=0.12 (5/40, GENOME_DK)
A=0.50 (8/16, Siberian)
G=0.50 (8/16, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: LOC100507053 : 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: 20231103111315

Population	Group	Sample Size	Ref Allele	Alt Allele	Ref HMOZ	Alt HMOZ	HTRZ	HWEP
Total	Global	18890	A=0.88354	G=0.11646	0.784436	0.017364	0.1982	8
European	Sub	14286	A=0.87393	G=0.12607	0.762985	0.01512	0.221896	0
African	Sub	2946	A=0.9671	G=0.0329	0.934827	0.000679	0.064494	0
African Others	Sub	114	A=0.991	G=0.009	0.982456	0.0	0.017544	0
African American	Sub	2832	A=0.9661	G=0.0339	0.93291	0.000706	0.066384	0
Asian	Sub	112	A=0.223	G=0.777	0.035714	0.589286	0.375	0
East Asian	Sub	86	A=0.23	G=0.77	0.023256	0.55814	0.418605	1
Other Asian	Sub	26	A=0.19	G=0.81	0.076923	0.692308	0.230769	1
Latin American 1	Sub	146	A=0.870	G=0.130	0.767123	0.027397	0.205479	0
Latin American 2	Sub	610	A=0.889	G=0.111	0.786885	0.009836	0.203279	0
South Asian	Sub	98	A=0.67	G=0.33	0.428571	0.081633	0.489796	0
Other	Sub	692	A=0.861	G=0.139	0.760116	0.037572	0.202312	5

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	A=0.880419	G=0.119581
gnomAD - Genomes	Global	Study-wide	140140	A=0.891230	G=0.108770
gnomAD - Genomes	European	Sub	75878	A=0.87825	G=0.12175
gnomAD - Genomes	African	Sub	42024	A=0.96773	G=0.03227
gnomAD - Genomes	American	Sub	13646	A=0.89360	G=0.10640
gnomAD - Genomes	Ashkenazi Jewish	Sub	3320	A=0.8232	G=0.1768
gnomAD - Genomes	East Asian	Sub	3120	A=0.2631	G=0.7369
gnomAD - Genomes	Other	Sub	2152	A=0.8555	G=0.1445
14KJPN	JAPANESE	Study-wide	28258	A=0.27267	G=0.72733
Allele Frequency Aggregator	Total	Global	18890	A=0.88354	G=0.11646
Allele Frequency Aggregator	European	Sub	14286	A=0.87393	G=0.12607
Allele Frequency Aggregator	African	Sub	2946	A=0.9671	G=0.0329
Allele Frequency Aggregator	Other	Sub	692	A=0.861	G=0.139
Allele Frequency Aggregator	Latin American 2	Sub	610	A=0.889	G=0.111
Allele Frequency Aggregator	Latin American 1	Sub	146	A=0.870	G=0.130
Allele Frequency Aggregator	Asian	Sub	112	A=0.223	G=0.777
Allele Frequency Aggregator	South Asian	Sub	98	A=0.67	G=0.33
8.3KJPN	JAPANESE	Study-wide	16760	A=0.27136	G=0.72864
1000Genomes_30x	Global	Study-wide	6404	A=0.7705	G=0.2295
1000Genomes_30x	African	Sub	1786	A=0.9882	G=0.0118
1000Genomes_30x	Europe	Sub	1266	A=0.8736	G=0.1264
1000Genomes_30x	South Asian	Sub	1202	A=0.6988	G=0.3012
1000Genomes_30x	East Asian	Sub	1170	A=0.2744	G=0.7256
1000Genomes_30x	American	Sub	980	A=0.920	G=0.080
1000Genomes	Global	Study-wide	5008	A=0.7522	G=0.2478
1000Genomes	African	Sub	1322	A=0.9856	G=0.0144
1000Genomes	East Asian	Sub	1008	A=0.2728	G=0.7272
1000Genomes	Europe	Sub	1006	A=0.8708	G=0.1292
1000Genomes	South Asian	Sub	978	A=0.694	G=0.306
1000Genomes	American	Sub	694	A=0.914	G=0.086
Genetic variation in the Estonian population	Estonian	Study-wide	4480	A=0.8859	G=0.1141
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.8627	G=0.1373
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.8706	G=0.1294
KOREAN population from KRGDB	KOREAN	Study-wide	2930	A=0.3137	G=0.6863, T=0.0000
Korean Genome Project	KOREAN	Study-wide	1832	A=0.2991	G=0.7009
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	A=0.873	G=0.127
Northern Sweden	ACPOP	Study-wide	600	A=0.912	G=0.088
Medical Genome Project healthy controls from Spanish population	Spanish controls	Study-wide	534	A=0.994	G=0.006
Qatari	Global	Study-wide	216	A=0.866	G=0.134
A Vietnamese Genetic Variation Database	Global	Study-wide	216	A=0.204	G=0.796
SGDP_PRJ	Global	Study-wide	208	A=0.370	G=0.630
The Danish reference pan genome	Danish	Study-wide	40	A=0.88	G=0.12
Siberian	Global	Study-wide	16	A=0.50	G=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 4	NC_000004.12:g.99109578A>G
GRCh38.p14 chr 4	NC_000004.12:g.99109578A>T
GRCh37.p13 chr 4	NC_000004.11:g.100030729A>G
GRCh37.p13 chr 4	NC_000004.11:g.100030729A>T

Gene: LOC100507053, uncharacterized LOC100507053 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC100507053 transcript	NR_037884.1:n.	N/A	Intron 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	A=	G	T
GRCh38.p14 chr 4	NC_000004.12:g.99109578=	NC_000004.12:g.99109578A>G	NC_000004.12:g.99109578A>T
GRCh37.p13 chr 4	NC_000004.11:g.100030729=	NC_000004.11:g.100030729A>G	NC_000004.11:g.100030729A>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, 20 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	BCMHGSC_JDW	ss92702738	Mar 24, 2008 (129)
2	COMPLETE_GENOMICS	ss166942534	Jul 04, 2010 (132)
3	BCM-HGSC-SUB	ss206668830	Jul 04, 2010 (132)
4	GMI	ss277843964	May 04, 2012 (137)
5	1000GENOMES	ss331831712	May 09, 2011 (134)
6	TISHKOFF	ss557720506	Apr 25, 2013 (138)
7	SSMP	ss651525077	Apr 25, 2013 (138)
8	EVA-GONL	ss980449010	Aug 21, 2014 (142)
9	JMKIDD_LAB	ss1071786404	Aug 21, 2014 (142)
10	1000GENOMES	ss1310976513	Aug 21, 2014 (142)
11	EVA_GENOME_DK	ss1580686884	Apr 01, 2015 (144)
12	EVA_DECODE	ss1589953042	Apr 01, 2015 (144)
13	EVA_UK10K_ALSPAC	ss1610734376	Apr 01, 2015 (144)
14	EVA_UK10K_TWINSUK	ss1653728409	Apr 01, 2015 (144)
15	EVA_MGP	ss1711067124	Apr 01, 2015 (144)
16	WEILL_CORNELL_DGM	ss1923689178	Feb 12, 2016 (147)
17	JJLAB	ss2022430435	Sep 14, 2016 (149)
18	USC_VALOUEV	ss2150559565	Dec 20, 2016 (150)
19	HUMAN_LONGEVITY	ss2265418298	Dec 20, 2016 (150)
20	SYSTEMSBIOZJU	ss2625714200	Nov 08, 2017 (151)
21	GRF	ss2706036609	Nov 08, 2017 (151)
22	GNOMAD	ss2812844416	Nov 08, 2017 (151)
23	SWEGEN	ss2995208814	Nov 08, 2017 (151)
24	BIOINF_KMB_FNS_UNIBA	ss3024990400	Nov 08, 2017 (151)
25	CSHL	ss3345861179	Nov 08, 2017 (151)
26	EGCUT_WGS	ss3663104613	Jul 13, 2019 (153)
27	EVA_DECODE	ss3712654949	Jul 13, 2019 (153)
28	ACPOP	ss3731420830	Jul 13, 2019 (153)
29	EVA	ss3762166121	Jul 13, 2019 (153)
30	KHV_HUMAN_GENOMES	ss3805314410	Jul 13, 2019 (153)
31	EVA	ss3828702876	Apr 26, 2020 (154)
32	SGDP_PRJ	ss3859608764	Apr 26, 2020 (154)
33	KRGDB	ss3905886113	Apr 26, 2020 (154)
34	KOGIC	ss3954740830	Apr 26, 2020 (154)
35	TOPMED	ss4624608908	Apr 26, 2021 (155)
36	TOMMO_GENOMICS	ss5167074743	Apr 26, 2021 (155)
37	1000G_HIGH_COVERAGE	ss5260285765	Oct 13, 2022 (156)
38	EVA	ss5350971365	Oct 13, 2022 (156)
39	HUGCELL_USP	ss5458928528	Oct 13, 2022 (156)
40	EVA	ss5507640880	Oct 13, 2022 (156)
41	1000G_HIGH_COVERAGE	ss5541952006	Oct 13, 2022 (156)
42	SANFORD_IMAGENETICS	ss5635663917	Oct 13, 2022 (156)
43	TOMMO_GENOMICS	ss5701804858	Oct 13, 2022 (156)
44	YY_MCH	ss5805353334	Oct 13, 2022 (156)
45	EVA	ss5844422834	Oct 13, 2022 (156)
46	EVA	ss5854355595	Oct 13, 2022 (156)
47	EVA	ss5864673820	Oct 13, 2022 (156)
48	EVA	ss5964054546	Oct 13, 2022 (156)
49	1000Genomes	NC_000004.11 - 100030729	Oct 12, 2018 (152)
50	1000Genomes_30x	NC_000004.12 - 99109578	Oct 13, 2022 (156)
51	The Avon Longitudinal Study of Parents and Children	NC_000004.11 - 100030729	Oct 12, 2018 (152)
52	Genetic variation in the Estonian population	NC_000004.11 - 100030729	Oct 12, 2018 (152)
53	The Danish reference pan genome	NC_000004.11 - 100030729	Apr 26, 2020 (154)
54	gnomAD - Genomes	NC_000004.12 - 99109578	Apr 26, 2021 (155)
55	Genome of the Netherlands Release 5	NC_000004.11 - 100030729	Apr 26, 2020 (154)
56	KOREAN population from KRGDB	NC_000004.11 - 100030729	Apr 26, 2020 (154)
57	Korean Genome Project	NC_000004.12 - 99109578	Apr 26, 2020 (154)
58	Medical Genome Project healthy controls from Spanish population	NC_000004.11 - 100030729	Apr 26, 2020 (154)
59	Northern Sweden	NC_000004.11 - 100030729	Jul 13, 2019 (153)
60	Qatari	NC_000004.11 - 100030729	Apr 26, 2020 (154)
61	SGDP_PRJ	NC_000004.11 - 100030729	Apr 26, 2020 (154)
62	Siberian	NC_000004.11 - 100030729	Apr 26, 2020 (154)
63	8.3KJPN	NC_000004.11 - 100030729	Apr 26, 2021 (155)
64	14KJPN	NC_000004.12 - 99109578	Oct 13, 2022 (156)
65	TopMed	NC_000004.12 - 99109578	Apr 26, 2021 (155)
66	UK 10K study - Twins	NC_000004.11 - 100030729	Oct 12, 2018 (152)
67	A Vietnamese Genetic Variation Database	NC_000004.11 - 100030729	Jul 13, 2019 (153)
68	ALFA	NC_000004.12 - 99109578	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
ss92702738, ss166942534, ss206668830, ss277843964, ss1589953042	NC_000004.10:100249751:A:G	NC_000004.12:99109577:A:G	(self)
22418567, 12470348, 8842861, 6851823, 5512508, 13063507, 182884, 4705695, 5731108, 11625744, 3075919, 25044050, 12470348, 2743978, ss331831712, ss557720506, ss651525077, ss980449010, ss1071786404, ss1310976513, ss1580686884, ss1610734376, ss1653728409, ss1711067124, ss1923689178, ss2022430435, ss2150559565, ss2625714200, ss2706036609, ss2812844416, ss2995208814, ss3345861179, ss3663104613, ss3731420830, ss3762166121, ss3828702876, ss3859608764, ss3905886113, ss5167074743, ss5350971365, ss5507640880, ss5635663917, ss5844422834, ss5964054546	NC_000004.11:100030728:A:G	NC_000004.12:99109577:A:G	(self)
29477941, 158807728, 11118831, 35641962, 461986464, 614228351, ss2265418298, ss3024990400, ss3712654949, ss3805314410, ss3954740830, ss4624608908, ss5260285765, ss5458928528, ss5541952006, ss5701804858, ss5805353334, ss5854355595, ss5864673820	NC_000004.12:99109577:A:G	NC_000004.12:99109577:A:G	(self)
13063507, ss3905886113	NC_000004.11:100030728:A:T	NC_000004.12:99109577:A: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 rs62323606

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

rs62323606