Name: rs1005958
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.

rs1005958

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr7:114662800 (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: G=0.311017 (82323/264690, TOPMED)
G=0.333898 (46721/139926, GnomAD)
G=0.38656 (14333/37078, ALFA) (+ 17 more)
G=0.06182 (1747/28258, 14KJPN)
G=0.06385 (1070/16758, 8.3KJPN)
G=0.2233 (1430/6404, 1000G_30x)
G=0.2240 (1122/5008, 1000G)
G=0.4900 (2195/4480, Estonian)
G=0.4616 (1779/3854, ALSPAC)
G=0.4668 (1731/3708, TWINSUK)
G=0.1150 (337/2930, KOREAN)
G=0.1157 (212/1832, Korea1K)
G=0.499 (498/998, GoNL)
G=0.442 (265/600, NorthernSweden)
G=0.269 (63/234, HapMap)
A=0.396 (88/222, SGDP_PRJ)
G=0.148 (32/216, Qatari)
G=0.159 (34/214, Vietnamese)
G=0.45 (18/40, GENOME_DK)
A=0.42 (15/36, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: FOXP2 : Intron Variant
Publications: 1 citation
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	37078	A=0.61344	G=0.38656
European	Sub	23806	A=0.54738	G=0.45262
African	Sub	4590	A=0.8599	G=0.1401
African Others	Sub	172	A=0.907	G=0.093
African American	Sub	4418	A=0.8581	G=0.1419
Asian	Sub	150	A=0.840	G=0.160
East Asian	Sub	116	A=0.853	G=0.147
Other Asian	Sub	34	A=0.79	G=0.21
Latin American 1	Sub	540	A=0.694	G=0.306
Latin American 2	Sub	4622	A=0.7029	G=0.2971
South Asian	Sub	144	A=0.701	G=0.299
Other	Sub	3226	A=0.5939	G=0.4061

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=0.688983	G=0.311017
gnomAD - Genomes	Global	Study-wide	139926	A=0.666102	G=0.333898
gnomAD - Genomes	European	Sub	75802	A=0.54722	G=0.45278
gnomAD - Genomes	African	Sub	41948	A=0.85391	G=0.14609
gnomAD - Genomes	American	Sub	13592	A=0.69092	G=0.30908
gnomAD - Genomes	Ashkenazi Jewish	Sub	3318	A=0.7155	G=0.2845
gnomAD - Genomes	East Asian	Sub	3116	A=0.8472	G=0.1528
gnomAD - Genomes	Other	Sub	2150	A=0.6977	G=0.3023
Allele Frequency Aggregator	Total	Global	37078	A=0.61344	G=0.38656
Allele Frequency Aggregator	European	Sub	23806	A=0.54738	G=0.45262
Allele Frequency Aggregator	Latin American 2	Sub	4622	A=0.7029	G=0.2971
Allele Frequency Aggregator	African	Sub	4590	A=0.8599	G=0.1401
Allele Frequency Aggregator	Other	Sub	3226	A=0.5939	G=0.4061
Allele Frequency Aggregator	Latin American 1	Sub	540	A=0.694	G=0.306
Allele Frequency Aggregator	Asian	Sub	150	A=0.840	G=0.160
Allele Frequency Aggregator	South Asian	Sub	144	A=0.701	G=0.299
14KJPN	JAPANESE	Study-wide	28258	A=0.93818	G=0.06182
8.3KJPN	JAPANESE	Study-wide	16758	A=0.93615	G=0.06385
1000Genomes_30x	Global	Study-wide	6404	A=0.7767	G=0.2233
1000Genomes_30x	African	Sub	1786	A=0.9199	G=0.0801
1000Genomes_30x	Europe	Sub	1266	A=0.5861	G=0.4139
1000Genomes_30x	South Asian	Sub	1202	A=0.7379	G=0.2621
1000Genomes_30x	East Asian	Sub	1170	A=0.8658	G=0.1342
1000Genomes_30x	American	Sub	980	A=0.703	G=0.297
1000Genomes	Global	Study-wide	5008	A=0.7760	G=0.2240
1000Genomes	African	Sub	1322	A=0.9107	G=0.0893
1000Genomes	East Asian	Sub	1008	A=0.8700	G=0.1300
1000Genomes	Europe	Sub	1006	A=0.5915	G=0.4085
1000Genomes	South Asian	Sub	978	A=0.733	G=0.267
1000Genomes	American	Sub	694	A=0.710	G=0.290
Genetic variation in the Estonian population	Estonian	Study-wide	4480	A=0.5100	G=0.4900
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.5384	G=0.4616
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.5332	G=0.4668
KOREAN population from KRGDB	KOREAN	Study-wide	2930	A=0.8850	G=0.1150
Korean Genome Project	KOREAN	Study-wide	1832	A=0.8843	G=0.1157
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	A=0.501	G=0.499
Northern Sweden	ACPOP	Study-wide	600	A=0.558	G=0.442
HapMap	Global	Study-wide	234	A=0.731	G=0.269
HapMap	American	Sub	120	A=0.517	G=0.483
HapMap	African	Sub	114	A=0.956	G=0.044
SGDP_PRJ	Global	Study-wide	222	A=0.396	G=0.604
Qatari	Global	Study-wide	216	A=0.852	G=0.148
A Vietnamese Genetic Variation Database	Global	Study-wide	214	A=0.841	G=0.159
The Danish reference pan genome	Danish	Study-wide	40	A=0.55	G=0.45
Siberian	Global	Study-wide	36	A=0.42	G=0.58

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.114662800A>G
GRCh37.p13 chr 7	NC_000007.13:g.114302855A>G
FOXP2 RefSeqGene	NG_007491.3:g.581491A>G

Gene: FOXP2, forkhead box P2 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
FOXP2 transcript variant 5	NM_001172766.3:c.1766+614… NM_001172766.3:c.1766+614A>G	N/A	Intron Variant
FOXP2 transcript variant 1	NM_014491.4:c.1769+614A>G	N/A	Intron Variant
FOXP2 transcript variant 2	NM_148898.4:c.1844+614A>G	N/A	Intron Variant
FOXP2 transcript variant 4	NM_148900.4:c.1820+614A>G	N/A	Intron Variant
FOXP2 transcript variant 6	NM_001172767.2:c.	N/A	Genic Downstream Transcript Variant
FOXP2 transcript variant 3	NM_148899.3:c.	N/A	Genic Downstream Transcript Variant
FOXP2 transcript variant 7	NR_033766.2:n.	N/A	Intron Variant
FOXP2 transcript variant 8	NR_033767.2: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
GRCh38.p14 chr 7	NC_000007.14:g.114662800=	NC_000007.14:g.114662800A>G
GRCh37.p13 chr 7	NC_000007.13:g.114302855=	NC_000007.13:g.114302855A>G
FOXP2 RefSeqGene	NG_007491.3:g.581491=	NG_007491.3:g.581491A>G
FOXP2 transcript variant 5	NM_001172766.2:c.1766+614=	NM_001172766.2:c.1766+614A>G
FOXP2 transcript variant 5	NM_001172766.3:c.1766+614=	NM_001172766.3:c.1766+614A>G
FOXP2 transcript variant 1	NM_014491.3:c.1769+614=	NM_014491.3:c.1769+614A>G
FOXP2 transcript variant 1	NM_014491.4:c.1769+614=	NM_014491.4:c.1769+614A>G
FOXP2 transcript variant 2	NM_148898.3:c.1844+614=	NM_148898.3:c.1844+614A>G
FOXP2 transcript variant 2	NM_148898.4:c.1844+614=	NM_148898.4:c.1844+614A>G
FOXP2 transcript variant 4	NM_148900.3:c.1820+614=	NM_148900.3:c.1820+614A>G
FOXP2 transcript variant 4	NM_148900.4:c.1820+614=	NM_148900.4:c.1820+614A>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#.

71 SubSNP, 20 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	TSC-CSHL	ss1467778	Oct 05, 2000 (86)
2	SC_JCM	ss6213235	Feb 20, 2003 (111)
3	CSHL-HAPMAP	ss17934739	Feb 27, 2004 (120)
4	ABI	ss44834979	Mar 14, 2006 (126)
5	AFFY	ss65970815	Nov 30, 2006 (127)
6	HGSV	ss82257904	Dec 16, 2007 (130)
7	BCMHGSC_JDW	ss93750338	Mar 24, 2008 (129)
8	HUMANGENOME_JCVI	ss98179682	Feb 06, 2009 (130)
9	1000GENOMES	ss112461352	Jan 25, 2009 (130)
10	ENSEMBL	ss142828833	Dec 01, 2009 (131)
11	ENSEMBL	ss143428073	Dec 01, 2009 (131)
12	ILLUMINA	ss159857785	Dec 01, 2009 (131)
13	BCM-HGSC-SUB	ss208396701	Jul 04, 2010 (132)
14	1000GENOMES	ss223279652	Jul 14, 2010 (132)
15	1000GENOMES	ss234129946	Jul 15, 2010 (132)
16	1000GENOMES	ss241052669	Jul 15, 2010 (132)
17	BL	ss254622488	May 09, 2011 (134)
18	GMI	ss279493541	May 04, 2012 (137)
19	PJP	ss293949433	May 09, 2011 (134)
20	ILLUMINA	ss479497699	Sep 08, 2015 (146)
21	TISHKOFF	ss560246177	Apr 25, 2013 (138)
22	SSMP	ss654651673	Apr 25, 2013 (138)
23	EVA-GONL	ss984695060	Aug 21, 2014 (142)
24	JMKIDD_LAB	ss1074906580	Aug 21, 2014 (142)
25	1000GENOMES	ss1326751879	Aug 21, 2014 (142)
26	DDI	ss1431251908	Apr 01, 2015 (144)
27	EVA_GENOME_DK	ss1582364220	Apr 01, 2015 (144)
28	EVA_DECODE	ss1594278230	Apr 01, 2015 (144)
29	EVA_UK10K_ALSPAC	ss1619009997	Apr 01, 2015 (144)
30	EVA_UK10K_TWINSUK	ss1662004030	Apr 01, 2015 (144)
31	HAMMER_LAB	ss1805178549	Sep 08, 2015 (146)
32	WEILL_CORNELL_DGM	ss1927957659	Feb 12, 2016 (147)
33	GENOMED	ss1970793302	Jul 19, 2016 (147)
34	JJLAB	ss2024662574	Sep 14, 2016 (149)
35	USC_VALOUEV	ss2152886450	Dec 20, 2016 (150)
36	HUMAN_LONGEVITY	ss2297040713	Dec 20, 2016 (150)
37	SYSTEMSBIOZJU	ss2626821175	Nov 08, 2017 (151)
38	GRF	ss2708601250	Nov 08, 2017 (151)
39	GNOMAD	ss2857990474	Nov 08, 2017 (151)
40	SWEGEN	ss3001880842	Nov 08, 2017 (151)
41	BIOINF_KMB_FNS_UNIBA	ss3026122269	Nov 08, 2017 (151)
42	CSHL	ss3347801367	Nov 08, 2017 (151)
43	ILLUMINA	ss3636872230	Oct 12, 2018 (152)
44	URBANLAB	ss3648732815	Oct 12, 2018 (152)
45	EGCUT_WGS	ss3669629241	Jul 13, 2019 (153)
46	EVA_DECODE	ss3720505074	Jul 13, 2019 (153)
47	ACPOP	ss3734989306	Jul 13, 2019 (153)
48	EVA	ss3767045860	Jul 13, 2019 (153)
49	PACBIO	ss3785933253	Jul 13, 2019 (153)
50	PACBIO	ss3791216211	Jul 13, 2019 (153)
51	PACBIO	ss3796096304	Jul 13, 2019 (153)
52	KHV_HUMAN_GENOMES	ss3810217961	Jul 13, 2019 (153)
53	EVA	ss3830772797	Apr 26, 2020 (154)
54	EVA	ss3838885427	Apr 26, 2020 (154)
55	EVA	ss3844341372	Apr 26, 2020 (154)
56	SGDP_PRJ	ss3868201737	Apr 26, 2020 (154)
57	KRGDB	ss3915526256	Apr 26, 2020 (154)
58	KOGIC	ss3962399788	Apr 26, 2020 (154)
59	TOPMED	ss4760247790	Apr 26, 2021 (155)
60	TOMMO_GENOMICS	ss5185150708	Apr 26, 2021 (155)
61	1000G_HIGH_COVERAGE	ss5274403522	Oct 14, 2022 (156)
62	HUGCELL_USP	ss5471323463	Oct 14, 2022 (156)
63	EVA	ss5509097558	Oct 14, 2022 (156)
64	1000G_HIGH_COVERAGE	ss5563377937	Oct 14, 2022 (156)
65	SANFORD_IMAGENETICS	ss5643797621	Oct 14, 2022 (156)
66	TOMMO_GENOMICS	ss5726017510	Oct 14, 2022 (156)
67	YY_MCH	ss5809013730	Oct 14, 2022 (156)
68	EVA	ss5823397454	Oct 14, 2022 (156)
69	EVA	ss5856059248	Oct 14, 2022 (156)
70	EVA	ss5860497481	Oct 14, 2022 (156)
71	EVA	ss5972983869	Oct 14, 2022 (156)
72	1000Genomes	NC_000007.13 - 114302855	Oct 12, 2018 (152)
73	1000Genomes_30x	NC_000007.14 - 114662800	Oct 14, 2022 (156)
74	The Avon Longitudinal Study of Parents and Children	NC_000007.13 - 114302855	Oct 12, 2018 (152)
75	Genetic variation in the Estonian population	NC_000007.13 - 114302855	Oct 12, 2018 (152)
76	The Danish reference pan genome	NC_000007.13 - 114302855	Apr 26, 2020 (154)
77	gnomAD - Genomes	NC_000007.14 - 114662800	Apr 26, 2021 (155)
78	Genome of the Netherlands Release 5	NC_000007.13 - 114302855	Apr 26, 2020 (154)
79	HapMap	NC_000007.14 - 114662800	Apr 26, 2020 (154)
80	KOREAN population from KRGDB	NC_000007.13 - 114302855	Apr 26, 2020 (154)
81	Korean Genome Project	NC_000007.14 - 114662800	Apr 26, 2020 (154)
82	Northern Sweden	NC_000007.13 - 114302855	Jul 13, 2019 (153)
83	Qatari	NC_000007.13 - 114302855	Apr 26, 2020 (154)
84	SGDP_PRJ	NC_000007.13 - 114302855	Apr 26, 2020 (154)
85	Siberian	NC_000007.13 - 114302855	Apr 26, 2020 (154)
86	8.3KJPN	NC_000007.13 - 114302855	Apr 26, 2021 (155)
87	14KJPN	NC_000007.14 - 114662800	Oct 14, 2022 (156)
88	TopMed	NC_000007.14 - 114662800	Apr 26, 2021 (155)
89	UK 10K study - Twins	NC_000007.13 - 114302855	Oct 12, 2018 (152)
90	A Vietnamese Genetic Variation Database	NC_000007.13 - 114302855	Jul 13, 2019 (153)
91	ALFA	NC_000007.14 - 114662800	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)
rs61678347	May 27, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss82257904	NC_000007.11:113896805:A:G	NC_000007.14:114662799:A:G	(self)
ss93750338, ss112461352, ss208396701, ss254622488, ss279493541, ss293949433, ss1594278230	NC_000007.12:114090090:A:G	NC_000007.14:114662799:A:G	(self)
38780782, 21573619, 15367489, 8529159, 9628240, 22703650, 8274171, 9999589, 20218717, 5402804, 43120015, 21573619, 4807332, ss223279652, ss234129946, ss241052669, ss479497699, ss560246177, ss654651673, ss984695060, ss1074906580, ss1326751879, ss1431251908, ss1582364220, ss1619009997, ss1662004030, ss1805178549, ss1927957659, ss1970793302, ss2024662574, ss2152886450, ss2626821175, ss2708601250, ss2857990474, ss3001880842, ss3347801367, ss3636872230, ss3669629241, ss3734989306, ss3767045860, ss3785933253, ss3791216211, ss3796096304, ss3830772797, ss3838885427, ss3868201737, ss3915526256, ss5185150708, ss5509097558, ss5643797621, ss5823397454, ss5972983869	NC_000007.13:114302854:A:G	NC_000007.14:114662799:A:G	(self)
50903872, 273755054, 3473806, 18777789, 59854614, 597625349, 2663688586, ss2297040713, ss3026122269, ss3648732815, ss3720505074, ss3810217961, ss3844341372, ss3962399788, ss4760247790, ss5274403522, ss5471323463, ss5563377937, ss5726017510, ss5809013730, ss5856059248, ss5860497481	NC_000007.14:114662799:A:G	NC_000007.14:114662799:A:G	(self)
ss17934739	NT_007933.13:39479544:A:G	NC_000007.14:114662799:A:G	(self)
ss1467778, ss6213235, ss44834979, ss65970815, ss98179682, ss142828833, ss143428073, ss159857785	NT_007933.15:52335697:A:G	NC_000007.14:114662799:A:G	(self)

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

1 citation for rs1005958

PMID	Title	Author	Year	Journal
27064276	Common Genetic Variants in FOXP2 Are Not Associated with Individual Differences in Language Development.	Mueller KL et al.	2016	PloS one

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

rs1005958