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dbSNP Short Genetic Variations

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.

rs1386488

Current Build 152

Released October 2, 2018

Organism
Homo sapiens
Position
chr12:71950838 (GRCh38.p12) 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
C>A / C>G
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.20081 (25215/125568, TOPMED)
C=0.2033 (6274/30854, GnomAD)
C=0.219 (1099/5008, 1000G) (+ 3 more)
C=0.177 (793/4480, Estonian)
C=0.177 (684/3854, ALSPAC)
C=0.187 (693/3708, TWINSUK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
TPH2 : Intron Variant
Publications
3 citations
Genomic View
See rs on genome
Help

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.p12 chr 12 NC_000012.12:g.71950838C>A
GRCh38.p12 chr 12 NC_000012.12:g.71950838C>G
GRCh37.p13 chr 12 NC_000012.11:g.72344618C>A
GRCh37.p13 chr 12 NC_000012.11:g.72344618C>G
TPH2 RefSeqGene NG_008279.1:g.16993C>A
TPH2 RefSeqGene NG_008279.1:g.16993C>G
Gene: TPH2, tryptophan hydroxylase 2 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
TPH2 transcript NM_173353.3:c. N/A Intron Variant
TPH2 transcript variant X1 XR_001748575.1:n. N/A Intron Variant
Help

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
Help

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").

Download
Study Population Group Sample Size Ref Allele Alt Allele
TopMed Global Study-wide 125568 C=0.20081 A=0.79919
gnomAD - Genomes Global Study-wide 30854 C=0.2033 A=0.7967
gnomAD - Genomes European Sub 18444 C=0.1811 A=0.8189
gnomAD - Genomes African Sub 8692 C=0.265 A=0.735
gnomAD - Genomes East Asian Sub 1602 C=0.172 A=0.828
gnomAD - Genomes Other Sub 978 C=0.18 A=0.82
gnomAD - Genomes American Sub 836 C=0.16 A=0.84
gnomAD - Genomes Ashkenazi Jewish Sub 302 C=0.16 A=0.84
1000Genomes Global Study-wide 5008 C=0.219 A=0.781
1000Genomes African Sub 1322 C=0.268 A=0.732
1000Genomes East Asian Sub 1008 C=0.186 A=0.814
1000Genomes Europe Sub 1006 C=0.183 A=0.817
1000Genomes South Asian Sub 978 C=0.24 A=0.76
1000Genomes American Sub 694 C=0.21 A=0.79
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.177 A=0.823
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.177 A=0.823
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.187 A=0.813
Help

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 C= A G Note
GRCh38.p12 chr 12 NC_000012.12:g.71...

NC_000012.12:g.71950838C=

NC_000012.12:g.71...

NC_000012.12:g.71950838C>A

NC_000012.12:g.71...

NC_000012.12:g.71950838C>G

GRCh37.p13 chr 12 NC_000012.11:g.72...

NC_000012.11:g.72344618C=

NC_000012.11:g.72...

NC_000012.11:g.72344618C>A

NC_000012.11:g.72...

NC_000012.11:g.72344618C>G

TPH2 RefSeqGene NG_008279.1:g.169...

NG_008279.1:g.16993C=

NG_008279.1:g.169...

NG_008279.1:g.16993C>A

NG_008279.1:g.169...

NG_008279.1:g.16993C>G

Help

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#.

95 SubSNP, 6 Frequency submissions
No Submitter Submission ID Date (Build)
1 TSC-CSHL ss2178615 Oct 23, 2000 (88)
2 SC_SNP ss16150723 Feb 27, 2004 (120)
3 CSHL-HAPMAP ss17456223 Feb 27, 2004 (120)
4 CSHL-HAPMAP ss19936601 Feb 27, 2004 (120)
5 SSAHASNP ss20977993 Apr 05, 2004 (121)
6 PERLEGEN ss23369678 Sep 20, 2004 (123)
7 ABI ss38960208 Mar 15, 2006 (126)
8 ILLUMINA ss65789519 Oct 14, 2006 (127)
9 ILLUMINA ss74996089 Dec 07, 2007 (129)
10 HGSV ss77181282 Dec 07, 2007 (129)
11 HGSV ss81469906 Dec 15, 2007 (130)
12 BCMHGSC_JDW ss89239177 Mar 24, 2008 (129)
13 HUMANGENOME_JCVI ss97238504 Feb 05, 2009 (130)
14 BGI ss103059313 Dec 01, 2009 (131)
15 1000GENOMES ss112142104 Jan 25, 2009 (130)
16 1000GENOMES ss113733685 Jan 25, 2009 (130)
17 ILLUMINA-UK ss118901228 Feb 14, 2009 (130)
18 KRIBB_YJKIM ss119390444 Dec 01, 2009 (131)
19 ENSEMBL ss137399424 Dec 01, 2009 (131)
20 GMI ss157627994 Dec 01, 2009 (131)
21 ILLUMINA ss160345643 Dec 01, 2009 (131)
22 COMPLETE_GENOMICS ss168494619 Jul 04, 2010 (132)
23 COMPLETE_GENOMICS ss170225528 Jul 04, 2010 (132)
24 ILLUMINA ss172462211 Jul 04, 2010 (132)
25 COMPLETE_GENOMICS ss175180710 Jul 04, 2010 (132)
26 BUSHMAN ss198378728 Jul 04, 2010 (132)
27 BCM-HGSC-SUB ss208030528 Jul 04, 2010 (132)
28 1000GENOMES ss225824072 Jul 14, 2010 (132)
29 1000GENOMES ss235986439 Jul 15, 2010 (132)
30 1000GENOMES ss242535941 Jul 15, 2010 (132)
31 BL ss255217695 May 09, 2011 (134)
32 GMI ss281450652 May 04, 2012 (137)
33 GMI ss286584468 Apr 25, 2013 (138)
34 PJP ss291279558 May 09, 2011 (134)
35 ILLUMINA ss410905998 Sep 17, 2011 (135)
36 ILLUMINA ss479951518 May 04, 2012 (137)
37 ILLUMINA ss479959907 May 04, 2012 (137)
38 ILLUMINA ss480600596 Sep 08, 2015 (146)
39 ILLUMINA ss484774025 May 04, 2012 (137)
40 ILLUMINA ss536862583 Sep 08, 2015 (146)
41 TISHKOFF ss563247334 Apr 25, 2013 (138)
42 SSMP ss658813274 Apr 25, 2013 (138)
43 ILLUMINA ss778429750 Sep 08, 2015 (146)
44 ILLUMINA ss782833688 Sep 08, 2015 (146)
45 ILLUMINA ss783798450 Sep 08, 2015 (146)
46 ILLUMINA ss832087244 Sep 08, 2015 (146)
47 ILLUMINA ss833885208 Sep 08, 2015 (146)
48 EVA-GONL ss989678091 Aug 21, 2014 (142)
49 JMKIDD_LAB ss1078565364 Aug 21, 2014 (142)
50 1000GENOMES ss1345572967 Aug 21, 2014 (142)
51 DDI ss1426976276 Apr 01, 2015 (144)
52 EVA_GENOME_DK ss1576366068 Apr 01, 2015 (144)
53 EVA_DECODE ss1599357442 Apr 01, 2015 (144)
54 EVA_UK10K_ALSPAC ss1628880739 Apr 01, 2015 (144)
55 EVA_UK10K_TWINSUK ss1671874772 Apr 01, 2015 (144)
56 EVA_SVP ss1713338339 Apr 01, 2015 (144)
57 ILLUMINA ss1752080366 Sep 08, 2015 (146)
58 HAMMER_LAB ss1807306065 Sep 08, 2015 (146)
59 WEILL_CORNELL_DGM ss1933041461 Feb 12, 2016 (147)
60 ILLUMINA ss1946343600 Feb 12, 2016 (147)
61 ILLUMINA ss1959447052 Feb 12, 2016 (147)
62 GENOMED ss1967621148 Jul 19, 2016 (147)
63 JJLAB ss2027271808 Sep 14, 2016 (149)
64 USC_VALOUEV ss2155615248 Dec 20, 2016 (150)
65 HUMAN_LONGEVITY ss2190935240 Dec 20, 2016 (150)
66 TOPMED ss2354915612 Dec 20, 2016 (150)
67 SYSTEMSBIOZJU ss2628118445 Nov 08, 2017 (151)
68 ILLUMINA ss2632976772 Nov 08, 2017 (151)
69 GRF ss2699965044 Nov 08, 2017 (151)
70 ILLUMINA ss2710765212 Nov 08, 2017 (151)
71 GNOMAD ss2912120660 Nov 08, 2017 (151)
72 AFFY ss2985621259 Nov 08, 2017 (151)
73 SWEGEN ss3009918759 Nov 08, 2017 (151)
74 ILLUMINA ss3021444198 Nov 08, 2017 (151)
75 BIOINF_KMB_FNS_UNIBA ss3027445850 Nov 08, 2017 (151)
76 TOPMED ss3174599340 Nov 08, 2017 (151)
77 TOPMED ss3174599341 Nov 08, 2017 (151)
78 CSHL ss3350128319 Nov 08, 2017 (151)
79 ILLUMINA ss3625626529 Oct 12, 2018 (152)
80 ILLUMINA ss3626910404 Oct 12, 2018 (152)
81 ILLUMINA ss3630984963 Oct 12, 2018 (152)
82 ILLUMINA ss3633025389 Oct 12, 2018 (152)
83 ILLUMINA ss3633726581 Oct 12, 2018 (152)
84 ILLUMINA ss3634512306 Oct 12, 2018 (152)
85 ILLUMINA ss3635417228 Oct 12, 2018 (152)
86 ILLUMINA ss3636197549 Oct 12, 2018 (152)
87 ILLUMINA ss3637168226 Oct 12, 2018 (152)
88 ILLUMINA ss3637971915 Oct 12, 2018 (152)
89 ILLUMINA ss3640219639 Oct 12, 2018 (152)
90 ILLUMINA ss3641031907 Oct 12, 2018 (152)
91 ILLUMINA ss3641326646 Oct 12, 2018 (152)
92 ILLUMINA ss3642964717 Oct 12, 2018 (152)
93 ILLUMINA ss3644596584 Oct 12, 2018 (152)
94 URBANLAB ss3649867926 Oct 12, 2018 (152)
95 ILLUMINA ss3651824919 Oct 12, 2018 (152)
96 1000Genomes NC_000012.11 - 72344618 Oct 12, 2018 (152)
97 The Avon Longitudinal Study of Parents and Children NC_000012.11 - 72344618 Oct 12, 2018 (152)
98 Genetic variation in the Estonian population NC_000012.11 - 72344618 Oct 12, 2018 (152)
99 gnomAD - Genomes NC_000012.11 - 72344618 Oct 12, 2018 (152)
100 TopMed NC_000012.12 - 71950838 Oct 12, 2018 (152)
101 UK 10K study - Twins NC_000012.11 - 72344618 Oct 12, 2018 (152)
Help

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)
rs59678709 May 25, 2008 (130)
Added to this RefSNP Cluster:
Submission ids Observation SPDI Canonical SPDI Source RSIDs
ss77181282, ss81469906 NC_000012.9:70630884:C= NC_000012.12:71950837:C= (self)
ss89239177, ss112142104, ss113733685, ss118901228, ss168494619, ss170225528, ss175180710, ss198378728, ss208030528, ss255217695, ss281450652, ss286584468, ss291279558, ss479951518, ss1599357442, ss1713338339, ss3642964717 NC_000012.10:70630884:C= NC_000012.12:71950837:C= (self)
58342935, 32394757, 22929037, 45822183, 32394757, ss225824072, ss235986439, ss242535941, ss479959907, ss480600596, ss484774025, ss536862583, ss563247334, ss658813274, ss778429750, ss782833688, ss783798450, ss832087244, ss833885208, ss989678091, ss1078565364, ss1345572967, ss1426976276, ss1576366068, ss1628880739, ss1671874772, ss1752080366, ss1807306065, ss1933041461, ss1946343600, ss1959447052, ss1967621148, ss2027271808, ss2155615248, ss2354915612, ss2628118445, ss2632976772, ss2699965044, ss2710765212, ss2912120660, ss2985621259, ss3009918759, ss3021444198, ss3350128319, ss3625626529, ss3626910404, ss3630984963, ss3633025389, ss3633726581, ss3634512306, ss3635417228, ss3636197549, ss3637168226, ss3637971915, ss3640219639, ss3641031907, ss3641326646, ss3644596584, ss3651824919 NC_000012.11:72344617:C= NC_000012.12:71950837:C= (self)
86864042, ss2190935240, ss3027445850, ss3174599340, ss3174599341, ss3649867926 NC_000012.12:71950837:C= NC_000012.12:71950837:C= (self)
ss16150723, ss17456223, ss19936601, ss20977993 NT_029419.10:34487923:C= NC_000012.12:71950837:C= (self)
ss2178615, ss23369678, ss38960208, ss65789519, ss74996089, ss97238504, ss103059313, ss119390444, ss137399424, ss157627994, ss160345643, ss172462211, ss410905998 NT_029419.12:34487923:C= NC_000012.12:71950837:C= (self)
ss77181282, ss81469906 NC_000012.9:70630884:C>A NC_000012.12:71950837:C>A (self)
ss89239177, ss112142104, ss113733685, ss118901228, ss168494619, ss170225528, ss175180710, ss198378728, ss208030528, ss255217695, ss281450652, ss286584468, ss291279558, ss479951518, ss1599357442, ss1713338339, ss3642964717 NC_000012.10:70630884:C>A NC_000012.12:71950837:C>A (self)
58342935, 32394757, 22929037, 45822183, 32394757, ss225824072, ss235986439, ss242535941, ss479959907, ss480600596, ss484774025, ss536862583, ss563247334, ss658813274, ss778429750, ss782833688, ss783798450, ss832087244, ss833885208, ss989678091, ss1078565364, ss1345572967, ss1426976276, ss1576366068, ss1628880739, ss1671874772, ss1752080366, ss1807306065, ss1933041461, ss1946343600, ss1959447052, ss1967621148, ss2027271808, ss2155615248, ss2354915612, ss2628118445, ss2632976772, ss2699965044, ss2710765212, ss2912120660, ss2985621259, ss3009918759, ss3021444198, ss3350128319, ss3625626529, ss3626910404, ss3630984963, ss3633025389, ss3633726581, ss3634512306, ss3635417228, ss3636197549, ss3637168226, ss3637971915, ss3640219639, ss3641031907, ss3641326646, ss3644596584, ss3651824919 NC_000012.11:72344617:C>A NC_000012.12:71950837:C>A (self)
86864042, ss2190935240, ss3027445850, ss3174599340, ss3649867926 NC_000012.12:71950837:C>A NC_000012.12:71950837:C>A (self)
ss16150723, ss17456223, ss19936601, ss20977993 NT_029419.10:34487923:C>A NC_000012.12:71950837:C>A (self)
ss2178615, ss23369678, ss38960208, ss65789519, ss74996089, ss97238504, ss103059313, ss119390444, ss137399424, ss157627994, ss160345643, ss172462211, ss410905998 NT_029419.12:34487923:C>A NC_000012.12:71950837:C>A (self)
ss3174599341 NC_000012.12:71950837:C>G NC_000012.12:71950837:C>G (self)
Help

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

3 citations for rs1386488
PMID Title Author Year Journal
19270759 Candidate genes and neuropsychological phenotypes in children with ADHD: review of association studies. Kebir O et al. 2009 Journal of psychiatry & neuroscience
21143251 A candidate gene association study of alcohol consumption in young women. Agrawal A et al. 2011 Alcoholism, clinical and experimental research
21910549 Genetic predictors of cue- and stress-induced cigarette craving: an exploratory study. Erblich J et al. 2012 Experimental and clinical psychopharmacology

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.

Software version is: 2.0.1.post76+b4aec9c