Name: rs58309597
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.

rs58309597

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr4:99150533 (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=0.176255 (46653/264690, TOPMED)
A=0.166743 (23355/140066, GnomAD)
G=0.27171 (7678/28258, 14KJPN) (+ 14 more)
A=0.16228 (3440/21198, ALFA)
G=0.26832 (4497/16760, 8.3KJPN)
A=0.2761 (1768/6404, 1000G_30x)
A=0.2891 (1448/5008, 1000G)
A=0.1493 (669/4480, Estonian)
G=0.3072 (900/2930, KOREAN)
G=0.2915 (534/1832, Korea1K)
A=0.127 (76/600, NorthernSweden)
G=0.385 (94/244, SGDP_PRJ)
A=0.148 (32/216, Qatari)
A=0.00 (0/46, Ancient Sardinia)
A=0.12 (5/40, GENOME_DK)
G=0.50 (9/18, Siberian)
A=0.50 (9/18, 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: 20230706150541

Population	Group	Sample Size	Ref Allele	Alt Allele
Total	Global	21198	G=0.83772	A=0.16228
European	Sub	14152	G=0.84412	A=0.15588
African	Sub	5526	G=0.8375	A=0.1625
African Others	Sub	198	G=0.843	A=0.157
African American	Sub	5328	G=0.8373	A=0.1627
Asian	Sub	112	G=0.214	A=0.786
East Asian	Sub	86	G=0.22	A=0.78
Other Asian	Sub	26	G=0.19	A=0.81
Latin American 1	Sub	146	G=0.842	A=0.158
Latin American 2	Sub	610	G=0.870	A=0.130
South Asian	Sub	98	G=0.70	A=0.30
Other	Sub	554	G=0.789	A=0.211

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=0.823745	A=0.176255
gnomAD - Genomes	Global	Study-wide	140066	G=0.833257	A=0.166743
gnomAD - Genomes	European	Sub	75888	G=0.84680	A=0.15320
gnomAD - Genomes	African	Sub	41964	G=0.83977	A=0.16023
gnomAD - Genomes	American	Sub	13628	G=0.87100	A=0.12900
gnomAD - Genomes	Ashkenazi Jewish	Sub	3316	G=0.8287	A=0.1713
gnomAD - Genomes	East Asian	Sub	3122	G=0.2687	A=0.7313
gnomAD - Genomes	Other	Sub	2148	G=0.8156	A=0.1844
14KJPN	JAPANESE	Study-wide	28258	G=0.27171	A=0.72829
Allele Frequency Aggregator	Total	Global	21198	G=0.83772	A=0.16228
Allele Frequency Aggregator	European	Sub	14152	G=0.84412	A=0.15588
Allele Frequency Aggregator	African	Sub	5526	G=0.8375	A=0.1625
Allele Frequency Aggregator	Latin American 2	Sub	610	G=0.870	A=0.130
Allele Frequency Aggregator	Other	Sub	554	G=0.789	A=0.211
Allele Frequency Aggregator	Latin American 1	Sub	146	G=0.842	A=0.158
Allele Frequency Aggregator	Asian	Sub	112	G=0.214	A=0.786
Allele Frequency Aggregator	South Asian	Sub	98	G=0.70	A=0.30
8.3KJPN	JAPANESE	Study-wide	16760	G=0.26832	A=0.73168
1000Genomes_30x	Global	Study-wide	6404	G=0.7239	A=0.2761
1000Genomes_30x	African	Sub	1786	G=0.8197	A=0.1803
1000Genomes_30x	Europe	Sub	1266	G=0.8531	A=0.1469
1000Genomes_30x	South Asian	Sub	1202	G=0.7304	A=0.2696
1000Genomes_30x	East Asian	Sub	1170	G=0.2761	A=0.7239
1000Genomes_30x	American	Sub	980	G=0.909	A=0.091
1000Genomes	Global	Study-wide	5008	G=0.7109	A=0.2891
1000Genomes	African	Sub	1322	G=0.8283	A=0.1717
1000Genomes	East Asian	Sub	1008	G=0.2738	A=0.7262
1000Genomes	Europe	Sub	1006	G=0.8519	A=0.1481
1000Genomes	South Asian	Sub	978	G=0.721	A=0.279
1000Genomes	American	Sub	694	G=0.903	A=0.097
Genetic variation in the Estonian population	Estonian	Study-wide	4480	G=0.8507	A=0.1493
KOREAN population from KRGDB	KOREAN	Study-wide	2930	G=0.3072	A=0.6928
Korean Genome Project	KOREAN	Study-wide	1832	G=0.2915	A=0.7085
Northern Sweden	ACPOP	Study-wide	600	G=0.873	A=0.127
SGDP_PRJ	Global	Study-wide	244	G=0.385	A=0.615
Qatari	Global	Study-wide	216	G=0.852	A=0.148
Ancient Sardinia genome-wide 1240k capture data generation and analysis	Global	Study-wide	46	G=1.00	A=0.00
The Danish reference pan genome	Danish	Study-wide	40	G=0.88	A=0.12
Siberian	Global	Study-wide	18	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 4	NC_000004.12:g.99150533G>A
GRCh37.p13 chr 4	NC_000004.11:g.100071690G>A

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	G=	A
GRCh38.p14 chr 4	NC_000004.12:g.99150533=	NC_000004.12:g.99150533G>A
GRCh37.p13 chr 4	NC_000004.11:g.100071690=	NC_000004.11:g.100071690G>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#.

43 SubSNP, 16 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	HGSV	ss83485513	Dec 15, 2007 (129)
2	HGSV	ss85483512	Dec 15, 2007 (129)
3	GMI	ss157649976	Dec 01, 2009 (131)
4	GMI	ss277844149	May 04, 2012 (137)
5	GMI	ss284967772	Apr 25, 2013 (138)
6	1000GENOMES	ss457318853	Sep 17, 2011 (135)
7	SSMP	ss651525364	Apr 25, 2013 (138)
8	JMKIDD_LAB	ss1071786707	Aug 21, 2014 (142)
9	1000GENOMES	ss1310977623	Aug 21, 2014 (142)
10	EVA_GENOME_DK	ss1580687160	Apr 01, 2015 (144)
11	EVA_DECODE	ss1589953431	Apr 01, 2015 (144)
12	WEILL_CORNELL_DGM	ss1923689600	Feb 12, 2016 (147)
13	JJLAB	ss2022430732	Sep 14, 2016 (149)
14	USC_VALOUEV	ss2150559884	Dec 20, 2016 (150)
15	HUMAN_LONGEVITY	ss2265420368	Dec 20, 2016 (150)
16	GRF	ss2706036836	Nov 08, 2017 (151)
17	GNOMAD	ss2812847638	Nov 08, 2017 (151)
18	AFFY	ss2985926606	Nov 08, 2017 (151)
19	SWEGEN	ss2995209514	Nov 08, 2017 (151)
20	CSHL	ss3345861530	Nov 08, 2017 (151)
21	EGCUT_WGS	ss3663105225	Jul 13, 2019 (153)
22	EVA_DECODE	ss3712655724	Jul 13, 2019 (153)
23	ACPOP	ss3731421261	Jul 13, 2019 (153)
24	EVA	ss3762166503	Jul 13, 2019 (153)
25	KHV_HUMAN_GENOMES	ss3805314883	Jul 13, 2019 (153)
26	EVA	ss3828703225	Apr 26, 2020 (154)
27	SGDP_PRJ	ss3859609475	Apr 26, 2020 (154)
28	KRGDB	ss3905886876	Apr 26, 2020 (154)
29	KOGIC	ss3954741367	Apr 26, 2020 (154)
30	EVA	ss3985085319	Apr 26, 2021 (155)
31	TOPMED	ss4624618137	Apr 26, 2021 (155)
32	TOMMO_GENOMICS	ss5167076065	Apr 26, 2021 (155)
33	1000G_HIGH_COVERAGE	ss5260286762	Oct 13, 2022 (156)
34	EVA	ss5350972898	Oct 13, 2022 (156)
35	HUGCELL_USP	ss5458929367	Oct 13, 2022 (156)
36	1000G_HIGH_COVERAGE	ss5541953461	Oct 13, 2022 (156)
37	SANFORD_IMAGENETICS	ss5635664583	Oct 13, 2022 (156)
38	TOMMO_GENOMICS	ss5701806549	Oct 13, 2022 (156)
39	YY_MCH	ss5805353621	Oct 13, 2022 (156)
40	EVA	ss5844423386	Oct 13, 2022 (156)
41	EVA	ss5854355764	Oct 13, 2022 (156)
42	EVA	ss5864674944	Oct 13, 2022 (156)
43	EVA	ss5964055169	Oct 13, 2022 (156)
44	1000Genomes	NC_000004.11 - 100071690	Oct 12, 2018 (152)
45	1000Genomes_30x	NC_000004.12 - 99150533	Oct 13, 2022 (156)
46	Genetic variation in the Estonian population	NC_000004.11 - 100071690	Oct 12, 2018 (152)
47	The Danish reference pan genome	NC_000004.11 - 100071690	Apr 26, 2020 (154)
48	gnomAD - Genomes	NC_000004.12 - 99150533	Apr 26, 2021 (155)
49	KOREAN population from KRGDB	NC_000004.11 - 100071690	Apr 26, 2020 (154)
50	Korean Genome Project	NC_000004.12 - 99150533	Apr 26, 2020 (154)
51	Northern Sweden	NC_000004.11 - 100071690	Jul 13, 2019 (153)
52	Ancient Sardinia genome-wide 1240k capture data generation and analysis	NC_000004.11 - 100071690	Apr 26, 2021 (155)
53	Qatari	NC_000004.11 - 100071690	Apr 26, 2020 (154)
54	SGDP_PRJ	NC_000004.11 - 100071690	Apr 26, 2020 (154)
55	Siberian	NC_000004.11 - 100071690	Apr 26, 2020 (154)
56	8.3KJPN	NC_000004.11 - 100071690	Apr 26, 2021 (155)
57	14KJPN	NC_000004.12 - 99150533	Oct 13, 2022 (156)
58	TopMed	NC_000004.12 - 99150533	Apr 26, 2021 (155)
59	ALFA	NC_000004.12 - 99150533	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
ss83485513, ss85483512	NC_000004.9:100428867:G:A	NC_000004.12:99150532:G:A	(self)
ss277844149, ss284967772, ss1589953431	NC_000004.10:100290712:G:A	NC_000004.12:99150532:G:A	(self)
22419741, 8843473, 6852099, 13064270, 4706126, 311246, 5731530, 11626455, 3076238, 25045372, ss457318853, ss651525364, ss1071786707, ss1310977623, ss1580687160, ss1923689600, ss2022430732, ss2150559884, ss2706036836, ss2812847638, ss2985926606, ss2995209514, ss3345861530, ss3663105225, ss3731421261, ss3762166503, ss3828703225, ss3859609475, ss3905886876, ss3985085319, ss5167076065, ss5350972898, ss5635664583, ss5844423386, ss5964055169	NC_000004.11:100071689:G:A	NC_000004.12:99150532:G:A	(self)
29479396, 158815890, 11119368, 35643653, 461995693, 7898521774, ss2265420368, ss3712655724, ss3805314883, ss3954741367, ss4624618137, ss5260286762, ss5458929367, ss5541953461, ss5701806549, ss5805353621, ss5854355764, ss5864674944	NC_000004.12:99150532:G:A	NC_000004.12:99150532:G:A	(self)
ss157649976	NT_016354.19:24619410:G:A	NC_000004.12:99150532: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 rs58309597

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

rs58309597