Name: rs4307239
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.

rs4307239

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr7:24314681 (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
Variation Type: SNV Single Nucleotide Variation
Frequency: A=0.447830 (118536/264690, TOPMED)
A=0.467365 (65290/139698, GnomAD)
A=0.19035 (5379/28258, 14KJPN) (+ 15 more)
A=0.49931 (9431/18888, ALFA)
A=0.18952 (3176/16758, 8.3KJPN)
A=0.3982 (2550/6404, 1000G_30x)
A=0.4024 (2015/5008, 1000G)
G=0.4761 (2132/4478, Estonian)
G=0.4561 (1758/3854, ALSPAC)
G=0.4601 (1706/3708, TWINSUK)
A=0.2154 (631/2930, KOREAN)
G=0.460 (459/998, GoNL)
G=0.452 (271/600, NorthernSweden)
A=0.266 (126/474, SGDP_PRJ)
A=0.361 (117/324, HapMap)
A=0.468 (101/216, Qatari)
G=0.28 (11/40, GENOME_DK)
A=0.28 (11/40, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: LOC107986777 : 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	18888	A=0.49931	G=0.50069
European	Sub	14284	A=0.53493	G=0.46507
African	Sub	2946	A=0.3534	G=0.6466
African Others	Sub	114	A=0.316	G=0.684
African American	Sub	2832	A=0.3549	G=0.6451
Asian	Sub	112	A=0.250	G=0.750
East Asian	Sub	86	A=0.27	G=0.73
Other Asian	Sub	26	A=0.19	G=0.81
Latin American 1	Sub	146	A=0.432	G=0.568
Latin American 2	Sub	610	A=0.467	G=0.533
South Asian	Sub	98	A=0.44	G=0.56
Other	Sub	692	A=0.477	G=0.523

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=0.447830	G=0.552170
gnomAD - Genomes	Global	Study-wide	139698	A=0.467365	G=0.532635
gnomAD - Genomes	European	Sub	75678	A=0.54173	G=0.45827
gnomAD - Genomes	African	Sub	41812	A=0.34856	G=0.65144
gnomAD - Genomes	American	Sub	13620	A=0.43341	G=0.56659
gnomAD - Genomes	Ashkenazi Jewish	Sub	3322	A=0.5816	G=0.4184
gnomAD - Genomes	East Asian	Sub	3114	A=0.2974	G=0.7026
gnomAD - Genomes	Other	Sub	2152	A=0.4452	G=0.5548
14KJPN	JAPANESE	Study-wide	28258	A=0.19035	G=0.80965
Allele Frequency Aggregator	Total	Global	18888	A=0.49931	G=0.50069
Allele Frequency Aggregator	European	Sub	14284	A=0.53493	G=0.46507
Allele Frequency Aggregator	African	Sub	2946	A=0.3534	G=0.6466
Allele Frequency Aggregator	Other	Sub	692	A=0.477	G=0.523
Allele Frequency Aggregator	Latin American 2	Sub	610	A=0.467	G=0.533
Allele Frequency Aggregator	Latin American 1	Sub	146	A=0.432	G=0.568
Allele Frequency Aggregator	Asian	Sub	112	A=0.250	G=0.750
Allele Frequency Aggregator	South Asian	Sub	98	A=0.44	G=0.56
8.3KJPN	JAPANESE	Study-wide	16758	A=0.18952	G=0.81048
1000Genomes_30x	Global	Study-wide	6404	A=0.3982	G=0.6018
1000Genomes_30x	African	Sub	1786	A=0.3326	G=0.6674
1000Genomes_30x	Europe	Sub	1266	A=0.5126	G=0.4874
1000Genomes_30x	South Asian	Sub	1202	A=0.4509	G=0.5491
1000Genomes_30x	East Asian	Sub	1170	A=0.2966	G=0.7034
1000Genomes_30x	American	Sub	980	A=0.427	G=0.573
1000Genomes	Global	Study-wide	5008	A=0.4024	G=0.5976
1000Genomes	African	Sub	1322	A=0.3306	G=0.6694
1000Genomes	East Asian	Sub	1008	A=0.3026	G=0.6974
1000Genomes	Europe	Sub	1006	A=0.5249	G=0.4751
1000Genomes	South Asian	Sub	978	A=0.459	G=0.541
1000Genomes	American	Sub	694	A=0.427	G=0.573
Genetic variation in the Estonian population	Estonian	Study-wide	4478	A=0.5239	G=0.4761
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.5439	G=0.4561
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.5399	G=0.4601
KOREAN population from KRGDB	KOREAN	Study-wide	2930	A=0.2154	G=0.7846
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	A=0.540	G=0.460
Northern Sweden	ACPOP	Study-wide	600	A=0.548	G=0.452
SGDP_PRJ	Global	Study-wide	474	A=0.266	G=0.734
HapMap	Global	Study-wide	324	A=0.361	G=0.639
HapMap	African	Sub	120	A=0.367	G=0.633
HapMap	American	Sub	114	A=0.518	G=0.482
HapMap	Asian	Sub	90	A=0.16	G=0.84
Qatari	Global	Study-wide	216	A=0.468	G=0.532
The Danish reference pan genome	Danish	Study-wide	40	A=0.72	G=0.28
Siberian	Global	Study-wide	40	A=0.28	G=0.72

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 7	NC_000007.14:g.24314681A>G
GRCh37.p13 chr 7	NC_000007.13:g.24354300A>G

Gene: LOC107986777, uncharacterized LOC107986777 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC107986777 transcript variant X3	XR_001745121.2:n.	N/A	Intron Variant
LOC107986777 transcript variant X7	XR_001745122.2:n.	N/A	Intron Variant
LOC107986777 transcript variant X8	XR_001745123.2:n.	N/A	Intron Variant
LOC107986777 transcript variant X10	XR_001745124.2:n.	N/A	Intron Variant
LOC107986777 transcript variant X11	XR_001745125.2:n.	N/A	Intron Variant
LOC107986777 transcript variant X13	XR_001745127.2:n.	N/A	Intron Variant
LOC107986777 transcript variant X9	XR_001745129.2:n.	N/A	Intron Variant
LOC107986777 transcript variant X4	XR_001745130.2:n.	N/A	Intron Variant
LOC107986777 transcript variant X14	XR_001745131.2:n.	N/A	Intron Variant
LOC107986777 transcript variant X15	XR_001745132.2:n.	N/A	Intron Variant
LOC107986777 transcript variant X1	XR_007060254.1:n.	N/A	Intron Variant
LOC107986777 transcript variant X2	XR_007060255.1:n.	N/A	Intron Variant
LOC107986777 transcript variant X5	XR_007060256.1:n.	N/A	Intron Variant
LOC107986777 transcript variant X6	XR_007060257.1:n.	N/A	Intron Variant
LOC107986777 transcript variant X12	XR_001745128.2:n.	N/A	Genic Upstream Transcript Variant
LOC107986777 transcript variant X16	XR_007060258.1:n.	N/A	Genic Upstream 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	A=	G
GRCh38.p14 chr 7	NC_000007.14:g.24314681=	NC_000007.14:g.24314681A>G
GRCh37.p13 chr 7	NC_000007.13:g.24354300=	NC_000007.13:g.24354300A>G

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#.

64 SubSNP, 18 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_JCM	ss5709540	Feb 20, 2003 (111)
2	WUGSC_SSAHASNP	ss14552654	Dec 05, 2003 (120)
3	SC_SNP	ss14860916	Dec 05, 2003 (120)
4	CSHL-HAPMAP	ss20305001	Feb 27, 2004 (120)
5	SSAHASNP	ss22590890	Apr 05, 2004 (121)
6	ABI	ss43054525	Mar 15, 2006 (126)
7	HGSV	ss84514815	Dec 15, 2007 (130)
8	HUMANGENOME_JCVI	ss98240159	Feb 05, 2009 (130)
9	BGI	ss105506752	Feb 05, 2009 (130)
10	1000GENOMES	ss111684160	Jan 25, 2009 (130)
11	1000GENOMES	ss113472111	Jan 25, 2009 (130)
12	GMI	ss154522722	Dec 01, 2009 (131)
13	COMPLETE_GENOMICS	ss163840396	Jul 04, 2010 (132)
14	BUSHMAN	ss203083847	Jul 04, 2010 (132)
15	1000GENOMES	ss222965989	Jul 14, 2010 (132)
16	1000GENOMES	ss233892303	Jul 15, 2010 (132)
17	1000GENOMES	ss240864551	Jul 15, 2010 (132)
18	GMI	ss279227448	May 04, 2012 (137)
19	PJP	ss294031555	May 09, 2011 (134)
20	TISHKOFF	ss559872661	Apr 25, 2013 (138)
21	SSMP	ss654225848	Apr 25, 2013 (138)
22	EVA-GONL	ss984058941	Aug 21, 2014 (142)
23	JMKIDD_LAB	ss1074447471	Aug 21, 2014 (142)
24	1000GENOMES	ss1324328348	Aug 21, 2014 (142)
25	DDI	ss1431059978	Apr 01, 2015 (144)
26	EVA_GENOME_DK	ss1582114520	Apr 01, 2015 (144)
27	EVA_DECODE	ss1593627755	Apr 01, 2015 (144)
28	EVA_UK10K_ALSPAC	ss1617784345	Apr 01, 2015 (144)
29	EVA_UK10K_TWINSUK	ss1660778378	Apr 01, 2015 (144)
30	HAMMER_LAB	ss1804914890	Sep 08, 2015 (146)
31	WEILL_CORNELL_DGM	ss1927304254	Feb 12, 2016 (147)
32	JJLAB	ss2024328807	Sep 14, 2016 (149)
33	USC_VALOUEV	ss2152525003	Dec 20, 2016 (150)
34	HUMAN_LONGEVITY	ss2292488966	Dec 20, 2016 (150)
35	SYSTEMSBIOZJU	ss2626653433	Nov 08, 2017 (151)
36	GRF	ss2708181898	Nov 08, 2017 (151)
37	GNOMAD	ss2850879444	Nov 08, 2017 (151)
38	SWEGEN	ss3000786975	Nov 08, 2017 (151)
39	BIOINF_KMB_FNS_UNIBA	ss3025958658	Nov 08, 2017 (151)
40	CSHL	ss3347485888	Nov 08, 2017 (151)
41	URBANLAB	ss3648584979	Oct 12, 2018 (152)
42	EGCUT_WGS	ss3668715363	Jul 13, 2019 (153)
43	EVA_DECODE	ss3719295514	Jul 13, 2019 (153)
44	ACPOP	ss3734447667	Jul 13, 2019 (153)
45	EVA	ss3766311019	Jul 13, 2019 (153)
46	KHV_HUMAN_GENOMES	ss3809478415	Jul 13, 2019 (153)
47	EVA	ss3830467987	Apr 26, 2020 (154)
48	EVA	ss3838721346	Apr 26, 2020 (154)
49	EVA	ss3844172563	Apr 26, 2020 (154)
50	SGDP_PRJ	ss3866843713	Apr 26, 2020 (154)
51	KRGDB	ss3913881534	Apr 26, 2020 (154)
52	TOPMED	ss4739025357	Apr 26, 2021 (155)
53	TOMMO_GENOMICS	ss5182249908	Apr 26, 2021 (155)
54	1000G_HIGH_COVERAGE	ss5272176868	Oct 14, 2022 (156)
55	EVA	ss5372279116	Oct 14, 2022 (156)
56	HUGCELL_USP	ss5469426572	Oct 14, 2022 (156)
57	1000G_HIGH_COVERAGE	ss5559994887	Oct 14, 2022 (156)
58	SANFORD_IMAGENETICS	ss5642547608	Oct 14, 2022 (156)
59	TOMMO_GENOMICS	ss5721826742	Oct 14, 2022 (156)
60	YY_MCH	ss5808423240	Oct 14, 2022 (156)
61	EVA	ss5822544637	Oct 14, 2022 (156)
62	EVA	ss5855807545	Oct 14, 2022 (156)
63	EVA	ss5858105348	Oct 14, 2022 (156)
64	EVA	ss5971747326	Oct 14, 2022 (156)
65	1000Genomes	NC_000007.13 - 24354300	Oct 12, 2018 (152)
66	1000Genomes_30x	NC_000007.14 - 24314681	Oct 14, 2022 (156)
67	The Avon Longitudinal Study of Parents and Children	NC_000007.13 - 24354300	Oct 12, 2018 (152)
68	Genetic variation in the Estonian population	NC_000007.13 - 24354300	Oct 12, 2018 (152)
69	The Danish reference pan genome	NC_000007.13 - 24354300	Apr 26, 2020 (154)
70	gnomAD - Genomes	NC_000007.14 - 24314681	Apr 26, 2021 (155)
71	Genome of the Netherlands Release 5	NC_000007.13 - 24354300	Apr 26, 2020 (154)
72	HapMap	NC_000007.14 - 24314681	Apr 26, 2020 (154)
73	KOREAN population from KRGDB	NC_000007.13 - 24354300	Apr 26, 2020 (154)
74	Northern Sweden	NC_000007.13 - 24354300	Jul 13, 2019 (153)
75	Qatari	NC_000007.13 - 24354300	Apr 26, 2020 (154)
76	SGDP_PRJ	NC_000007.13 - 24354300	Apr 26, 2020 (154)
77	Siberian	NC_000007.13 - 24354300	Apr 26, 2020 (154)
78	8.3KJPN	NC_000007.13 - 24354300	Apr 26, 2021 (155)
79	14KJPN	NC_000007.14 - 24314681	Oct 14, 2022 (156)
80	TopMed	NC_000007.14 - 24314681	Apr 26, 2021 (155)
81	UK 10K study - Twins	NC_000007.13 - 24354300	Oct 12, 2018 (152)
82	ALFA	NC_000007.14 - 24314681	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)
rs10347373	Feb 27, 2004 (120)
rs10480029	Feb 27, 2004 (120)
rs59209504	May 25, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss84514815	NC_000007.11:24127539:A:G	NC_000007.14:24314680:A:G	(self)
ss111684160, ss113472111, ss163840396, ss203083847, ss279227448, ss294031555, ss1593627755	NC_000007.12:24320824:A:G	NC_000007.14:24314680:A:G	(self)
36269685, 20219298, 14453611, 8279459, 9014689, 21058928, 7732532, 9346184, 18860693, 5041357, 40219215, 20219298, ss222965989, ss233892303, ss240864551, ss559872661, ss654225848, ss984058941, ss1074447471, ss1324328348, ss1431059978, ss1582114520, ss1617784345, ss1660778378, ss1804914890, ss1927304254, ss2024328807, ss2152525003, ss2626653433, ss2708181898, ss2850879444, ss3000786975, ss3347485888, ss3668715363, ss3734447667, ss3766311019, ss3830467987, ss3838721346, ss3866843713, ss3913881534, ss5182249908, ss5372279116, ss5642547608, ss5822544637, ss5971747326	NC_000007.13:24354299:A:G	NC_000007.14:24314680:A:G	(self)
47520822, 255744869, 3357792, 55663846, 576402916, 11333831091, ss2292488966, ss3025958658, ss3648584979, ss3719295514, ss3809478415, ss3844172563, ss4739025357, ss5272176868, ss5469426572, ss5559994887, ss5721826742, ss5808423240, ss5855807545, ss5858105348	NC_000007.14:24314680:A:G	NC_000007.14:24314680:A:G	(self)
ss14552654, ss14860916, ss20305001, ss22590890	NT_007819.14:23647907:A:G	NC_000007.14:24314680:A:G	(self)
ss5709540, ss43054525, ss98240159, ss105506752, ss154522722	NT_007819.17:24344299:A:G	NC_000007.14:24314680:A:G	(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 rs4307239

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

rs4307239