Name: rs4760749
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.

rs4760749

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr12:71958328 (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 / G>C / G>T
Variation Type: SNV Single Nucleotide Variation
Frequency: G=0.171503 (45395/264690, TOPMED)
G=0.176299 (24702/140114, GnomAD)
G=0.02077 (587/28258, 14KJPN) (+ 17 more)
G=0.15887 (3001/18890, ALFA)
G=0.02184 (366/16760, 8.3KJPN)
G=0.1423 (911/6404, 1000G_30x)
G=0.1374 (688/5008, 1000G)
G=0.1489 (667/4480, Estonian)
G=0.1463 (564/3854, ALSPAC)
G=0.1532 (568/3708, TWINSUK)
G=0.0386 (113/2930, KOREAN)
G=0.0355 (65/1832, Korea1K)
G=0.156 (156/998, GoNL)
G=0.093 (56/600, NorthernSweden)
G=0.098 (52/530, SGDP_PRJ)
G=0.110 (36/326, HapMap)
G=0.190 (41/216, Qatari)
G=0.060 (13/216, Vietnamese)
G=0.07 (4/56, Siberian)
G=0.15 (6/40, GENOME_DK)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: TPH2 : 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	18890	G=0.15887	C=0.84113
European	Sub	14286	G=0.14812	C=0.85188
African	Sub	2946	G=0.2288	C=0.7712
African Others	Sub	114	G=0.246	C=0.754
African American	Sub	2832	G=0.2281	C=0.7719
Asian	Sub	112	G=0.018	C=0.982
East Asian	Sub	86	G=0.01	C=0.99
Other Asian	Sub	26	G=0.04	C=0.96
Latin American 1	Sub	146	G=0.178	C=0.822
Latin American 2	Sub	610	G=0.095	C=0.905
South Asian	Sub	98	G=0.07	C=0.93
Other	Sub	692	G=0.171	C=0.829

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=0.171503	C=0.828497
gnomAD - Genomes	Global	Study-wide	140114	G=0.176299	C=0.823701
gnomAD - Genomes	European	Sub	75930	G=0.15448	C=0.84552
gnomAD - Genomes	African	Sub	41922	G=0.24763	C=0.75237
gnomAD - Genomes	American	Sub	13650	G=0.12300	C=0.87700
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	G=0.1267	C=0.8733
gnomAD - Genomes	East Asian	Sub	3134	G=0.0434	C=0.9566
gnomAD - Genomes	Other	Sub	2154	G=0.1648	C=0.8352
14KJPN	JAPANESE	Study-wide	28258	G=0.02077	C=0.97923
Allele Frequency Aggregator	Total	Global	18890	G=0.15887	C=0.84113
Allele Frequency Aggregator	European	Sub	14286	G=0.14812	C=0.85188
Allele Frequency Aggregator	African	Sub	2946	G=0.2288	C=0.7712
Allele Frequency Aggregator	Other	Sub	692	G=0.171	C=0.829
Allele Frequency Aggregator	Latin American 2	Sub	610	G=0.095	C=0.905
Allele Frequency Aggregator	Latin American 1	Sub	146	G=0.178	C=0.822
Allele Frequency Aggregator	Asian	Sub	112	G=0.018	C=0.982
Allele Frequency Aggregator	South Asian	Sub	98	G=0.07	C=0.93
8.3KJPN	JAPANESE	Study-wide	16760	G=0.02184	C=0.97816
1000Genomes_30x	Global	Study-wide	6404	G=0.1423	C=0.8577
1000Genomes_30x	African	Sub	1786	G=0.2335	C=0.7665
1000Genomes_30x	Europe	Sub	1266	G=0.1453	C=0.8547
1000Genomes_30x	South Asian	Sub	1202	G=0.0749	C=0.9251
1000Genomes_30x	East Asian	Sub	1170	G=0.0530	C=0.9470
1000Genomes_30x	American	Sub	980	G=0.161	C=0.839
1000Genomes	Global	Study-wide	5008	G=0.1374	C=0.8626
1000Genomes	African	Sub	1322	G=0.2322	C=0.7678
1000Genomes	East Asian	Sub	1008	G=0.0526	C=0.9474
1000Genomes	Europe	Sub	1006	G=0.1481	C=0.8519
1000Genomes	South Asian	Sub	978	G=0.075	C=0.925
1000Genomes	American	Sub	694	G=0.153	C=0.847
Genetic variation in the Estonian population	Estonian	Study-wide	4480	G=0.1489	C=0.8511
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.1463	C=0.8537
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.1532	C=0.8468
KOREAN population from KRGDB	KOREAN	Study-wide	2930	G=0.0386	A=0.0000, C=0.9614, T=0.0000
Korean Genome Project	KOREAN	Study-wide	1832	G=0.0355	C=0.9645
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	G=0.156	C=0.844
Northern Sweden	ACPOP	Study-wide	600	G=0.093	C=0.907
SGDP_PRJ	Global	Study-wide	530	G=0.098	C=0.902
HapMap	Global	Study-wide	326	G=0.110	C=0.890
HapMap	African	Sub	118	G=0.186	C=0.814
HapMap	American	Sub	118	G=0.119	C=0.881
HapMap	Asian	Sub	90	G=0.00	C=1.00
Qatari	Global	Study-wide	216	G=0.190	C=0.810
A Vietnamese Genetic Variation Database	Global	Study-wide	216	G=0.060	C=0.940
Siberian	Global	Study-wide	56	G=0.07	C=0.93
The Danish reference pan genome	Danish	Study-wide	40	G=0.15	C=0.85

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.71958328G>A
GRCh38.p14 chr 12	NC_000012.12:g.71958328G>C
GRCh38.p14 chr 12	NC_000012.12:g.71958328G>T
GRCh37.p13 chr 12	NC_000012.11:g.72352108G>A
GRCh37.p13 chr 12	NC_000012.11:g.72352108G>C
GRCh37.p13 chr 12	NC_000012.11:g.72352108G>T
TPH2 RefSeqGene	NG_008279.1:g.24483G>A
TPH2 RefSeqGene	NG_008279.1:g.24483G>C
TPH2 RefSeqGene	NG_008279.1:g.24483G>T

Gene: TPH2, tryptophan hydroxylase 2 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
TPH2 transcript	NM_173353.4:c.608+8673G>A	N/A	Intron Variant
TPH2 transcript variant X1	XR_001748575.2: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	G=	A	C	T
GRCh38.p14 chr 12	NC_000012.12:g.71958328=	NC_000012.12:g.71958328G>A	NC_000012.12:g.71958328G>C	NC_000012.12:g.71958328G>T
GRCh37.p13 chr 12	NC_000012.11:g.72352108=	NC_000012.11:g.72352108G>A	NC_000012.11:g.72352108G>C	NC_000012.11:g.72352108G>T
TPH2 RefSeqGene	NG_008279.1:g.24483=	NG_008279.1:g.24483G>A	NG_008279.1:g.24483G>C	NG_008279.1:g.24483G>T
TPH2 transcript	NM_173353.3:c.608+8673=	NM_173353.3:c.608+8673G>A	NM_173353.3:c.608+8673G>C	NM_173353.3:c.608+8673G>T
TPH2 transcript	NM_173353.4:c.608+8673=	NM_173353.4:c.608+8673G>A	NM_173353.4:c.608+8673G>C	NM_173353.4:c.608+8673G>T
TPH2 transcript variant X1	XM_005268642.1:c.626+8673=	XM_005268642.1:c.626+8673G>A	XM_005268642.1:c.626+8673G>C	XM_005268642.1:c.626+8673G>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#.

78 SubSNP, 20 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	WI_SSAHASNP	ss6566404	Feb 20, 2003 (111)
2	SC_SNP	ss15668213	Feb 27, 2004 (120)
3	SSAHASNP	ss20946336	Apr 05, 2004 (121)
4	PERLEGEN	ss23369791	Sep 20, 2004 (123)
5	ABI	ss40126616	Mar 15, 2006 (126)
6	HGSV	ss77343738	Dec 06, 2007 (129)
7	HGSV	ss82692902	Dec 15, 2007 (130)
8	BCMHGSC_JDW	ss89239212	Mar 24, 2008 (129)
9	HUMANGENOME_JCVI	ss97238515	Feb 06, 2009 (130)
10	BGI	ss106814898	Feb 06, 2009 (130)
11	1000GENOMES	ss112142203	Jan 25, 2009 (130)
12	1000GENOMES	ss113733782	Jan 25, 2009 (130)
13	ILLUMINA-UK	ss118901280	Feb 14, 2009 (130)
14	ENSEMBL	ss133239548	Dec 01, 2009 (131)
15	ENSEMBL	ss137399400	Dec 01, 2009 (131)
16	GMI	ss157628077	Dec 01, 2009 (131)
17	COMPLETE_GENOMICS	ss168494724	Jul 04, 2010 (132)
18	COMPLETE_GENOMICS	ss170225791	Jul 04, 2010 (132)
19	COMPLETE_GENOMICS	ss175180735	Jul 04, 2010 (132)
20	BUSHMAN	ss198378812	Jul 04, 2010 (132)
21	BCM-HGSC-SUB	ss208098879	Jul 04, 2010 (132)
22	1000GENOMES	ss225824097	Jul 14, 2010 (132)
23	1000GENOMES	ss235986457	Jul 15, 2010 (132)
24	1000GENOMES	ss242535955	Jul 15, 2010 (132)
25	BL	ss255217752	May 09, 2011 (134)
26	GMI	ss281450669	May 04, 2012 (137)
27	GMI	ss286584480	Apr 25, 2013 (138)
28	PJP	ss291279570	May 09, 2011 (134)
29	TISHKOFF	ss563247371	Apr 25, 2013 (138)
30	SSMP	ss658813312	Apr 25, 2013 (138)
31	EVA-GONL	ss989678154	Aug 21, 2014 (142)
32	JMKIDD_LAB	ss1078565408	Aug 21, 2014 (142)
33	1000GENOMES	ss1345573148	Aug 21, 2014 (142)
34	DDI	ss1426976288	Apr 01, 2015 (144)
35	EVA_GENOME_DK	ss1576366087	Apr 01, 2015 (144)
36	EVA_DECODE	ss1599357498	Apr 01, 2015 (144)
37	EVA_UK10K_ALSPAC	ss1628880857	Apr 01, 2015 (144)
38	EVA_UK10K_TWINSUK	ss1671874890	Apr 01, 2015 (144)
39	HAMMER_LAB	ss1807306093	Sep 08, 2015 (146)
40	WEILL_CORNELL_DGM	ss1933041506	Feb 12, 2016 (147)
41	GENOMED	ss1967621162	Jul 19, 2016 (147)
42	JJLAB	ss2027271831	Sep 14, 2016 (149)
43	USC_VALOUEV	ss2155615272	Dec 20, 2016 (150)
44	HUMAN_LONGEVITY	ss2190935669	Dec 20, 2016 (150)
45	SYSTEMSBIOZJU	ss2628118461	Nov 08, 2017 (151)
46	GRF	ss2699965068	Nov 08, 2017 (151)
47	GNOMAD	ss2912121224	Nov 08, 2017 (151)
48	SWEGEN	ss3009918828	Nov 08, 2017 (151)
49	BIOINF_KMB_FNS_UNIBA	ss3027445865	Nov 08, 2017 (151)
50	CSHL	ss3350128339	Nov 08, 2017 (151)
51	URBANLAB	ss3649867940	Oct 12, 2018 (152)
52	EGCUT_WGS	ss3677190858	Jul 13, 2019 (153)
53	EVA_DECODE	ss3693944320	Jul 13, 2019 (153)
54	ACPOP	ss3739143668	Jul 13, 2019 (153)
55	EVA	ss3750646497	Jul 13, 2019 (153)
56	PACBIO	ss3787265144	Jul 13, 2019 (153)
57	PACBIO	ss3792360109	Jul 13, 2019 (153)
58	PACBIO	ss3797242964	Jul 13, 2019 (153)
59	KHV_HUMAN_GENOMES	ss3815980526	Jul 13, 2019 (153)
60	EVA	ss3833193446	Apr 27, 2020 (154)
61	EVA	ss3840167408	Apr 27, 2020 (154)
62	EVA	ss3845654610	Apr 27, 2020 (154)
63	SGDP_PRJ	ss3878564998	Apr 27, 2020 (154)
64	KRGDB	ss3927237621	Apr 27, 2020 (154)
65	KOGIC	ss3972213257	Apr 27, 2020 (154)
66	TOPMED	ss4923251953	Apr 26, 2021 (155)
67	TOMMO_GENOMICS	ss5206961135	Apr 26, 2021 (155)
68	1000G_HIGH_COVERAGE	ss5291301626	Oct 16, 2022 (156)
69	EVA	ss5406525475	Oct 16, 2022 (156)
70	HUGCELL_USP	ss5485997407	Oct 16, 2022 (156)
71	1000G_HIGH_COVERAGE	ss5589036558	Oct 16, 2022 (156)
72	SANFORD_IMAGENETICS	ss5653430219	Oct 16, 2022 (156)
73	TOMMO_GENOMICS	ss5756940318	Oct 16, 2022 (156)
74	YY_MCH	ss5813418569	Oct 16, 2022 (156)
75	EVA	ss5838154471	Oct 16, 2022 (156)
76	EVA	ss5850438102	Oct 16, 2022 (156)
77	EVA	ss5904948334	Oct 16, 2022 (156)
78	EVA	ss5944804087	Oct 16, 2022 (156)
79	1000Genomes	NC_000012.11 - 72352108	Oct 12, 2018 (152)
80	1000Genomes_30x	NC_000012.12 - 71958328	Oct 16, 2022 (156)
81	The Avon Longitudinal Study of Parents and Children	NC_000012.11 - 72352108	Oct 12, 2018 (152)
82	Genetic variation in the Estonian population	NC_000012.11 - 72352108	Oct 12, 2018 (152)
83	The Danish reference pan genome	NC_000012.11 - 72352108	Apr 27, 2020 (154)
84	gnomAD - Genomes	NC_000012.12 - 71958328	Apr 26, 2021 (155)
85	Genome of the Netherlands Release 5	NC_000012.11 - 72352108	Apr 27, 2020 (154)
86	HapMap	NC_000012.12 - 71958328	Apr 27, 2020 (154)
87	KOREAN population from KRGDB	NC_000012.11 - 72352108	Apr 27, 2020 (154)
88	Korean Genome Project	NC_000012.12 - 71958328	Apr 27, 2020 (154)
89	Northern Sweden	NC_000012.11 - 72352108	Jul 13, 2019 (153)
90	Qatari	NC_000012.11 - 72352108	Apr 27, 2020 (154)
91	SGDP_PRJ	NC_000012.11 - 72352108	Apr 27, 2020 (154)
92	Siberian	NC_000012.11 - 72352108	Apr 27, 2020 (154)
93	8.3KJPN	NC_000012.11 - 72352108	Apr 26, 2021 (155)
94	14KJPN	NC_000012.12 - 71958328	Oct 16, 2022 (156)
95	TopMed	NC_000012.12 - 71958328	Apr 26, 2021 (155)
96	UK 10K study - Twins	NC_000012.11 - 72352108	Oct 12, 2018 (152)
97	A Vietnamese Genetic Variation Database	NC_000012.11 - 72352108	Jul 13, 2019 (153)
98	ALFA	NC_000012.12 - 71958328	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)
rs60306045	May 25, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
34415015, ss3927237621	NC_000012.11:72352107:G:A	NC_000012.12:71958327:G:A	(self)
ss77343738, ss82692902	NC_000012.9:70638374:G:C	NC_000012.12:71958327:G:C	(self)
ss89239212, ss112142203, ss113733782, ss118901280, ss168494724, ss170225791, ss175180735, ss198378812, ss208098879, ss255217752, ss281450669, ss286584480, ss291279570, ss1599357498	NC_000012.10:70638374:G:C	NC_000012.12:71958327:G:C	(self)
58343120, 32394886, 22929106, 3019363, 14453526, 34415015, 12428533, 15083436, 30581978, 8131626, 64930442, 32394886, 7189181, ss225824097, ss235986457, ss242535955, ss563247371, ss658813312, ss989678154, ss1078565408, ss1345573148, ss1426976288, ss1576366087, ss1628880857, ss1671874890, ss1807306093, ss1933041506, ss1967621162, ss2027271831, ss2155615272, ss2628118461, ss2699965068, ss2912121224, ss3009918828, ss3350128339, ss3677190858, ss3739143668, ss3750646497, ss3787265144, ss3792360109, ss3797242964, ss3833193446, ss3840167408, ss3878564998, ss3927237621, ss5206961135, ss5406525475, ss5653430219, ss5838154471, ss5944804087	NC_000012.11:72352107:G:C	NC_000012.12:71958327:G:C	(self)
76562493, 411454258, 847209, 28591258, 90777422, 138797610, 3847934653, ss2190935669, ss3027445865, ss3649867940, ss3693944320, ss3815980526, ss3845654610, ss3972213257, ss4923251953, ss5291301626, ss5485997407, ss5589036558, ss5756940318, ss5813418569, ss5850438102, ss5904948334	NC_000012.12:71958327:G:C	NC_000012.12:71958327:G:C	(self)
ss15668213, ss20946336	NT_029419.10:34495413:G:C	NC_000012.12:71958327:G:C	(self)
ss6566404, ss23369791, ss40126616, ss97238515, ss106814898, ss133239548, ss137399400, ss157628077	NT_029419.12:34495413:G:C	NC_000012.12:71958327:G:C	(self)
34415015, ss3927237621	NC_000012.11:72352107:G:T	NC_000012.12:71958327:G: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 rs4760749

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

rs4760749