Name: rs10879352
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.

rs10879352

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr12:72013178 (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: T>A / T>C / T>G
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.435627 (115306/264690, TOPMED)
T=0.442993 (62012/139984, GnomAD)
T=0.33265 (9400/28258, 14KJPN) (+ 17 more)
T=0.42845 (11665/27226, ALFA)
T=0.33252 (5573/16760, 8.3KJPN)
T=0.4165 (2667/6404, 1000G_30x)
T=0.4123 (2065/5008, 1000G)
T=0.4074 (1825/4480, Estonian)
T=0.3988 (1537/3854, ALSPAC)
T=0.4153 (1540/3708, TWINSUK)
T=0.3423 (1003/2930, KOREAN)
T=0.4498 (851/1892, HapMap)
T=0.3384 (620/1832, Korea1K)
T=0.408 (407/998, GoNL)
T=0.357 (214/600, NorthernSweden)
T=0.280 (129/460, SGDP_PRJ)
T=0.435 (94/216, Qatari)
T=0.406 (86/212, Vietnamese)
T=0.40 (16/40, GENOME_DK)
T=0.34 (13/38, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: TPH2 : 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	27226	T=0.42845	C=0.57155
European	Sub	17350	T=0.41153	C=0.58847
African	Sub	4788	T=0.5330	C=0.4670
African Others	Sub	160	T=0.556	C=0.444
African American	Sub	4628	T=0.5322	C=0.4678
Asian	Sub	172	T=0.372	C=0.628
East Asian	Sub	112	T=0.375	C=0.625
Other Asian	Sub	60	T=0.37	C=0.63
Latin American 1	Sub	314	T=0.443	C=0.557
Latin American 2	Sub	2826	T=0.3698	C=0.6302
South Asian	Sub	110	T=0.291	C=0.709
Other	Sub	1666	T=0.4160	C=0.5840

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	T=0.435627	C=0.564373
gnomAD - Genomes	Global	Study-wide	139984	T=0.442993	C=0.557007
gnomAD - Genomes	European	Sub	75816	T=0.41857	C=0.58143
gnomAD - Genomes	African	Sub	41938	T=0.52461	C=0.47539
gnomAD - Genomes	American	Sub	13636	T=0.36770	C=0.63230
gnomAD - Genomes	Ashkenazi Jewish	Sub	3320	T=0.3533	C=0.6467
gnomAD - Genomes	East Asian	Sub	3124	T=0.3784	C=0.6216
gnomAD - Genomes	Other	Sub	2150	T=0.4223	C=0.5777
14KJPN	JAPANESE	Study-wide	28258	T=0.33265	C=0.66735
Allele Frequency Aggregator	Total	Global	27226	T=0.42845	C=0.57155
Allele Frequency Aggregator	European	Sub	17350	T=0.41153	C=0.58847
Allele Frequency Aggregator	African	Sub	4788	T=0.5330	C=0.4670
Allele Frequency Aggregator	Latin American 2	Sub	2826	T=0.3698	C=0.6302
Allele Frequency Aggregator	Other	Sub	1666	T=0.4160	C=0.5840
Allele Frequency Aggregator	Latin American 1	Sub	314	T=0.443	C=0.557
Allele Frequency Aggregator	Asian	Sub	172	T=0.372	C=0.628
Allele Frequency Aggregator	South Asian	Sub	110	T=0.291	C=0.709
8.3KJPN	JAPANESE	Study-wide	16760	T=0.33252	C=0.66748
1000Genomes_30x	Global	Study-wide	6404	T=0.4165	C=0.5835
1000Genomes_30x	African	Sub	1786	T=0.5487	C=0.4513
1000Genomes_30x	Europe	Sub	1266	T=0.3878	C=0.6122
1000Genomes_30x	South Asian	Sub	1202	T=0.2845	C=0.7155
1000Genomes_30x	East Asian	Sub	1170	T=0.3761	C=0.6239
1000Genomes_30x	American	Sub	980	T=0.422	C=0.578
1000Genomes	Global	Study-wide	5008	T=0.4123	C=0.5877
1000Genomes	African	Sub	1322	T=0.5461	C=0.4539
1000Genomes	East Asian	Sub	1008	T=0.3720	C=0.6280
1000Genomes	Europe	Sub	1006	T=0.3956	C=0.6044
1000Genomes	South Asian	Sub	978	T=0.285	C=0.715
1000Genomes	American	Sub	694	T=0.419	C=0.581
Genetic variation in the Estonian population	Estonian	Study-wide	4480	T=0.4074	C=0.5926
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.3988	C=0.6012
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.4153	C=0.5847
KOREAN population from KRGDB	KOREAN	Study-wide	2930	T=0.3423	A=0.0000, C=0.6577, G=0.0000
HapMap	Global	Study-wide	1892	T=0.4498	C=0.5502
HapMap	American	Sub	770	T=0.388	C=0.612
HapMap	African	Sub	692	T=0.565	C=0.435
HapMap	Asian	Sub	254	T=0.343	C=0.657
HapMap	Europe	Sub	176	T=0.420	C=0.580
Korean Genome Project	KOREAN	Study-wide	1832	T=0.3384	C=0.6616
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.408	C=0.592
Northern Sweden	ACPOP	Study-wide	600	T=0.357	C=0.643
SGDP_PRJ	Global	Study-wide	460	T=0.280	C=0.720
Qatari	Global	Study-wide	216	T=0.435	C=0.565
A Vietnamese Genetic Variation Database	Global	Study-wide	212	T=0.406	C=0.594
The Danish reference pan genome	Danish	Study-wide	40	T=0.40	C=0.60
Siberian	Global	Study-wide	38	T=0.34	C=0.66

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 12	NC_000012.12:g.72013178T>A
GRCh38.p14 chr 12	NC_000012.12:g.72013178T>C
GRCh38.p14 chr 12	NC_000012.12:g.72013178T>G
GRCh37.p13 chr 12	NC_000012.11:g.72406958T>A
GRCh37.p13 chr 12	NC_000012.11:g.72406958T>C
GRCh37.p13 chr 12	NC_000012.11:g.72406958T>G
TPH2 RefSeqGene	NG_008279.1:g.79333T>A
TPH2 RefSeqGene	NG_008279.1:g.79333T>C
TPH2 RefSeqGene	NG_008279.1:g.79333T>G

Gene: TPH2, tryptophan hydroxylase 2 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
TPH2 transcript	NM_173353.4:c.1069-9221T>A	N/A	Intron Variant
TPH2 transcript variant X1	XR_001748575.2:n.	N/A	Genic Downstream 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	T=	A	C	G
GRCh38.p14 chr 12	NC_000012.12:g.72013178=	NC_000012.12:g.72013178T>A	NC_000012.12:g.72013178T>C	NC_000012.12:g.72013178T>G
GRCh37.p13 chr 12	NC_000012.11:g.72406958=	NC_000012.11:g.72406958T>A	NC_000012.11:g.72406958T>C	NC_000012.11:g.72406958T>G
TPH2 RefSeqGene	NG_008279.1:g.79333=	NG_008279.1:g.79333T>A	NG_008279.1:g.79333T>C	NG_008279.1:g.79333T>G
TPH2 transcript	NM_173353.3:c.1069-9221=	NM_173353.3:c.1069-9221T>A	NM_173353.3:c.1069-9221T>C	NM_173353.3:c.1069-9221T>G
TPH2 transcript	NM_173353.4:c.1069-9221=	NM_173353.4:c.1069-9221T>A	NM_173353.4:c.1069-9221T>C	NM_173353.4:c.1069-9221T>G
TPH2 transcript variant X1	XM_005268642.1:c.1087-9221=	XM_005268642.1:c.1087-9221T>A	XM_005268642.1:c.1087-9221T>C	XM_005268642.1:c.1087-9221T>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#.

85 SubSNP, 20 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_SNP	ss15941153	Feb 27, 2004 (120)
2	SC_SNP	ss18548715	Feb 27, 2004 (120)
3	SC_SNP	ss19004715	Feb 27, 2004 (120)
4	PERLEGEN	ss23962831	Sep 20, 2004 (123)
5	PERLEGEN	ss69113003	May 17, 2007 (127)
6	ILLUMINA	ss74991876	Dec 06, 2007 (129)
7	AFFY	ss76501781	Dec 06, 2007 (129)
8	HGSV	ss78265584	Dec 06, 2007 (129)
9	BCMHGSC_JDW	ss89239519	Mar 24, 2008 (129)
10	HUMANGENOME_JCVI	ss97320316	Feb 05, 2009 (130)
11	BGI	ss106814941	Feb 05, 2009 (130)
12	1000GENOMES	ss112143169	Jan 25, 2009 (130)
13	1000GENOMES	ss113734816	Jan 25, 2009 (130)
14	ILLUMINA-UK	ss118901588	Feb 14, 2009 (130)
15	KRIBB_YJKIM	ss119646869	Dec 01, 2009 (131)
16	ENSEMBL	ss142470103	Dec 01, 2009 (131)
17	GMI	ss157628999	Dec 01, 2009 (131)
18	COMPLETE_GENOMICS	ss168495875	Jul 04, 2010 (132)
19	COMPLETE_GENOMICS	ss170229122	Jul 04, 2010 (132)
20	ILLUMINA	ss170693034	Jul 04, 2010 (132)
21	COMPLETE_GENOMICS	ss175181014	Jul 04, 2010 (132)
22	BUSHMAN	ss198379462	Jul 04, 2010 (132)
23	1000GENOMES	ss225824343	Jul 14, 2010 (132)
24	1000GENOMES	ss235986626	Jul 15, 2010 (132)
25	1000GENOMES	ss242536138	Jul 15, 2010 (132)
26	GMI	ss281450876	May 04, 2012 (137)
27	GMI	ss286584575	Apr 25, 2013 (138)
28	PJP	ss291279673	May 09, 2011 (134)
29	ILLUMINA	ss536647665	Sep 08, 2015 (146)
30	TISHKOFF	ss563247650	Apr 25, 2013 (138)
31	SSMP	ss658813583	Apr 25, 2013 (138)
32	EVA-GONL	ss989678551	Aug 21, 2014 (142)
33	JMKIDD_LAB	ss1078565731	Aug 21, 2014 (142)
34	1000GENOMES	ss1345574637	Aug 21, 2014 (142)
35	DDI	ss1426976425	Apr 01, 2015 (144)
36	EVA_GENOME_DK	ss1576366315	Apr 01, 2015 (144)
37	EVA_DECODE	ss1599357904	Apr 01, 2015 (144)
38	EVA_UK10K_ALSPAC	ss1628881759	Apr 01, 2015 (144)
39	EVA_UK10K_TWINSUK	ss1671875792	Apr 01, 2015 (144)
40	EVA_SVP	ss1713338393	Apr 01, 2015 (144)
41	HAMMER_LAB	ss1807306318	Sep 08, 2015 (146)
42	WEILL_CORNELL_DGM	ss1933041910	Feb 12, 2016 (147)
43	GENOMED	ss1967621334	Jul 19, 2016 (147)
44	JJLAB	ss2027272049	Sep 14, 2016 (149)
45	USC_VALOUEV	ss2155615511	Dec 20, 2016 (150)
46	HUMAN_LONGEVITY	ss2190938791	Dec 20, 2016 (150)
47	SYSTEMSBIOZJU	ss2628118648	Nov 08, 2017 (151)
48	GRF	ss2699965332	Nov 08, 2017 (151)
49	GNOMAD	ss2912125258	Nov 08, 2017 (151)
50	SWEGEN	ss3009919403	Nov 08, 2017 (151)
51	BIOINF_KMB_FNS_UNIBA	ss3027445994	Nov 08, 2017 (151)
52	CSHL	ss3350128499	Nov 08, 2017 (151)
53	ILLUMINA	ss3626910506	Oct 12, 2018 (152)
54	ILLUMINA	ss3637971949	Oct 12, 2018 (152)
55	ILLUMINA	ss3642964747	Oct 12, 2018 (152)
56	URBANLAB	ss3649868052	Oct 12, 2018 (152)
57	EGCUT_WGS	ss3677191482	Jul 13, 2019 (153)
58	EVA_DECODE	ss3693944964	Jul 13, 2019 (153)
59	ACPOP	ss3739143972	Jul 13, 2019 (153)
60	EVA	ss3750647049	Jul 13, 2019 (153)
61	PACBIO	ss3787265314	Jul 13, 2019 (153)
62	PACBIO	ss3792360262	Jul 13, 2019 (153)
63	PACBIO	ss3797243116	Jul 13, 2019 (153)
64	KHV_HUMAN_GENOMES	ss3815981044	Jul 13, 2019 (153)
65	EVA	ss3833193623	Apr 27, 2020 (154)
66	EVA	ss3840167513	Apr 27, 2020 (154)
67	EVA	ss3845654715	Apr 27, 2020 (154)
68	SGDP_PRJ	ss3878565723	Apr 27, 2020 (154)
69	KRGDB	ss3927238443	Apr 27, 2020 (154)
70	KOGIC	ss3972213948	Apr 27, 2020 (154)
71	EVA	ss4017596777	Apr 26, 2021 (155)
72	TOPMED	ss4923265011	Apr 26, 2021 (155)
73	TOMMO_GENOMICS	ss5206962656	Apr 26, 2021 (155)
74	1000G_HIGH_COVERAGE	ss5291302782	Oct 16, 2022 (156)
75	EVA	ss5406527913	Oct 16, 2022 (156)
76	HUGCELL_USP	ss5485998533	Oct 16, 2022 (156)
77	EVA	ss5510752449	Oct 16, 2022 (156)
78	1000G_HIGH_COVERAGE	ss5589038436	Oct 16, 2022 (156)
79	SANFORD_IMAGENETICS	ss5653430944	Oct 16, 2022 (156)
80	TOMMO_GENOMICS	ss5756942231	Oct 16, 2022 (156)
81	YY_MCH	ss5813418926	Oct 16, 2022 (156)
82	EVA	ss5838154988	Oct 16, 2022 (156)
83	EVA	ss5850438311	Oct 16, 2022 (156)
84	EVA	ss5904949850	Oct 16, 2022 (156)
85	EVA	ss5944804887	Oct 16, 2022 (156)
86	1000Genomes	NC_000012.11 - 72406958	Oct 12, 2018 (152)
87	1000Genomes_30x	NC_000012.12 - 72013178	Oct 16, 2022 (156)
88	The Avon Longitudinal Study of Parents and Children	NC_000012.11 - 72406958	Oct 12, 2018 (152)
89	Genetic variation in the Estonian population	NC_000012.11 - 72406958	Oct 12, 2018 (152)
90	The Danish reference pan genome	NC_000012.11 - 72406958	Apr 27, 2020 (154)
91	gnomAD - Genomes	NC_000012.12 - 72013178	Apr 26, 2021 (155)
92	Genome of the Netherlands Release 5	NC_000012.11 - 72406958	Apr 27, 2020 (154)
93	HapMap	NC_000012.12 - 72013178	Apr 27, 2020 (154)
94	KOREAN population from KRGDB	NC_000012.11 - 72406958	Apr 27, 2020 (154)
95	Korean Genome Project	NC_000012.12 - 72013178	Apr 27, 2020 (154)
96	Northern Sweden	NC_000012.11 - 72406958	Jul 13, 2019 (153)
97	Qatari	NC_000012.11 - 72406958	Apr 27, 2020 (154)
98	SGDP_PRJ	NC_000012.11 - 72406958	Apr 27, 2020 (154)
99	Siberian	NC_000012.11 - 72406958	Apr 27, 2020 (154)
100	8.3KJPN	NC_000012.11 - 72406958	Apr 26, 2021 (155)
101	14KJPN	NC_000012.12 - 72013178	Oct 16, 2022 (156)
102	TopMed	NC_000012.12 - 72013178	Apr 26, 2021 (155)
103	UK 10K study - Twins	NC_000012.11 - 72406958	Oct 12, 2018 (152)
104	A Vietnamese Genetic Variation Database	NC_000012.11 - 72406958	Jul 13, 2019 (153)
105	ALFA	NC_000012.12 - 72013178	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
34415837, ss3927238443	NC_000012.11:72406957:T:A	NC_000012.12:72013177:T:A	(self)
ss78265584	NC_000012.9:70693224:T:C	NC_000012.12:72013177:T:C	(self)
ss89239519, ss112143169, ss113734816, ss118901588, ss168495875, ss170229122, ss175181014, ss198379462, ss281450876, ss286584575, ss291279673, ss1599357904, ss1713338393, ss3642964747	NC_000012.10:70693224:T:C	NC_000012.12:72013177:T:C	(self)
58344656, 32395861, 22929730, 3019566, 14453902, 34415837, 12428837, 15083840, 30582703, 8131865, 64931963, 32395861, 7189432, ss225824343, ss235986626, ss242536138, ss536647665, ss563247650, ss658813583, ss989678551, ss1078565731, ss1345574637, ss1426976425, ss1576366315, ss1628881759, ss1671875792, ss1807306318, ss1933041910, ss1967621334, ss2027272049, ss2155615511, ss2628118648, ss2699965332, ss2912125258, ss3009919403, ss3350128499, ss3626910506, ss3637971949, ss3677191482, ss3739143972, ss3750647049, ss3787265314, ss3792360262, ss3797243116, ss3833193623, ss3840167513, ss3878565723, ss3927238443, ss4017596777, ss5206962656, ss5406527913, ss5510752449, ss5653430944, ss5838154988, ss5944804887	NC_000012.11:72406957:T:C	NC_000012.12:72013177:T:C	(self)
76564371, 411464686, 847335, 28591949, 90779335, 138810668, 12776589420, ss2190938791, ss3027445994, ss3649868052, ss3693944964, ss3815981044, ss3845654715, ss3972213948, ss4923265011, ss5291302782, ss5485998533, ss5589038436, ss5756942231, ss5813418926, ss5850438311, ss5904949850	NC_000012.12:72013177:T:C	NC_000012.12:72013177:T:C	(self)
ss15941153, ss18548715, ss19004715	NT_029419.10:34550263:T:C	NC_000012.12:72013177:T:C	(self)
ss23962831, ss69113003, ss74991876, ss76501781, ss97320316, ss106814941, ss119646869, ss142470103, ss157628999, ss170693034	NT_029419.12:34550263:T:C	NC_000012.12:72013177:T:C	(self)
34415837, ss3927238443	NC_000012.11:72406957:T:G	NC_000012.12:72013177:T: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 rs10879352

PMID	Title	Author	Year	Journal
18937842	The influence of serotonin- and other genes on impulsive behavioral aggression and cognitive impulsivity in children with attention-deficit/hyperactivity disorder (ADHD): Findings from a family-based association test (FBAT) analysis.	Oades RD et al.	2008	Behavioral and brain functions

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

rs10879352