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dbSNP Short Genetic Variations

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.

rs118092776

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr12:102912801 (GRCh38.p13) 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>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.001496 (396/264690, TOPMED)
T=0.001679 (422/251382, GnomAD_exome)
T=0.001475 (341/231228, ALFA) (+ 15 more)
T=0.000913 (128/140198, GnomAD)
T=0.001747 (212/121382, ExAC)
T=0.00492 (387/78702, PAGE_STUDY)
T=0.05113 (857/16760, 8.3KJPN)
T=0.00062 (8/13006, GO-ESP)
T=0.0030 (15/5008, 1000G)
T=0.0004 (2/4480, Estonian)
T=0.0021 (8/3854, ALSPAC)
T=0.0008 (3/3708, TWINSUK)
T=0.0342 (100/2922, KOREAN)
T=0.0289 (53/1832, Korea1K)
T=0.015 (12/792, PRJEB37584)
T=0.002 (1/534, MGP)
C=0.5 (2/4, SGDP_PRJ)
T=0.5 (2/4, SGDP_PRJ)
Clinical Significance
Reported in ClinVar
Gene : Consequence
PAH : Missense Variant
Publications
2 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.p13 chr 12 NC_000012.12:g.102912801C>T
GRCh37.p13 chr 12 NC_000012.11:g.103306579C>T
PAH RefSeqGene NG_008690.2:g.50610G>A
Gene: PAH, phenylalanine hydroxylase (minus strand)
Molecule type Change Amino acid[Codon] SO Term
PAH transcript variant 1 NM_000277.3:c.158G>A R [CGC] > H [CAC] Coding Sequence Variant
phenylalanine-4-hydroxylase NP_000268.1:p.Arg53His R (Arg) > H (His) Missense Variant
PAH transcript variant 2 NM_001354304.2:c.158G>A R [CGC] > H [CAC] Coding Sequence Variant
phenylalanine-4-hydroxylase NP_001341233.1:p.Arg53His R (Arg) > H (His) Missense Variant
PAH transcript variant X1 XM_017019370.2:c.158G>A R [CGC] > H [CAC] Coding Sequence Variant
phenylalanine-4-hydroxylase isoform X1 XP_016874859.1:p.Arg53His R (Arg) > H (His) Missense 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.

Allele: T (allele ID: 108337 )
ClinVar Accession Disease Names Clinical Significance
RCV000088842.4 not provided Not-Provided
RCV000490373.10 Phenylketonuria Uncertain-Significance
RCV001175359.1 not specified Likely-Benign

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: 20201027095038
Population Group Sample Size Ref Allele Alt Allele
Total Global 231228 C=0.998525 T=0.001475
European Sub 200800 C=0.999233 T=0.000767
African Sub 5146 C=0.9996 T=0.0004
African Others Sub 186 C=1.000 T=0.000
African American Sub 4960 C=0.9996 T=0.0004
Asian Sub 6404 C=0.9803 T=0.0197
East Asian Sub 4554 C=0.9767 T=0.0233
Other Asian Sub 1850 C=0.9892 T=0.0108
Latin American 1 Sub 814 C=1.000 T=0.000
Latin American 2 Sub 1042 C=0.9971 T=0.0029
South Asian Sub 296 C=1.000 T=0.000
Other Sub 16726 C=0.99665 T=0.00335


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 264690 C=0.998504 T=0.001496
gnomAD - Exomes Global Study-wide 251382 C=0.998321 T=0.001679
gnomAD - Exomes European Sub 135316 C=0.999416 T=0.000584
gnomAD - Exomes Asian Sub 49006 C=0.99392 T=0.00608
gnomAD - Exomes American Sub 34590 C=0.99905 T=0.00095
gnomAD - Exomes African Sub 16256 C=0.99982 T=0.00018
gnomAD - Exomes Ashkenazi Jewish Sub 10078 C=0.99990 T=0.00010
gnomAD - Exomes Other Sub 6136 C=0.9987 T=0.0013
gnomAD - Genomes Global Study-wide 140198 C=0.999087 T=0.000913
gnomAD - Genomes European Sub 75942 C=0.99949 T=0.00051
gnomAD - Genomes African Sub 42012 C=0.99976 T=0.00024
gnomAD - Genomes American Sub 13642 C=0.99780 T=0.00220
gnomAD - Genomes Ashkenazi Jewish Sub 3322 C=1.0000 T=0.0000
gnomAD - Genomes East Asian Sub 3128 C=0.9853 T=0.0147
gnomAD - Genomes Other Sub 2152 C=0.9986 T=0.0014
ExAC Global Study-wide 121382 C=0.998253 T=0.001747
ExAC Europe Sub 73336 C=0.99937 T=0.00063
ExAC Asian Sub 25156 C=0.99364 T=0.00636
ExAC American Sub 11578 C=0.99965 T=0.00035
ExAC African Sub 10404 C=0.99990 T=0.00010
ExAC Other Sub 908 C=0.999 T=0.001
The PAGE Study Global Study-wide 78702 C=0.99508 T=0.00492
The PAGE Study AfricanAmerican Sub 32516 C=0.99985 T=0.00015
The PAGE Study Mexican Sub 10810 C=0.99926 T=0.00074
The PAGE Study Asian Sub 8318 C=0.9598 T=0.0402
The PAGE Study PuertoRican Sub 7918 C=1.0000 T=0.0000
The PAGE Study NativeHawaiian Sub 4534 C=0.9956 T=0.0044
The PAGE Study Cuban Sub 4230 C=0.9988 T=0.0012
The PAGE Study Dominican Sub 3828 C=0.9984 T=0.0016
The PAGE Study CentralAmerican Sub 2450 C=0.9992 T=0.0008
The PAGE Study SouthAmerican Sub 1982 C=0.9985 T=0.0015
The PAGE Study NativeAmerican Sub 1260 C=0.9984 T=0.0016
The PAGE Study SouthAsian Sub 856 C=0.998 T=0.002
8.3KJPN JAPANESE Study-wide 16760 C=0.94887 T=0.05113
GO Exome Sequencing Project Global Study-wide 13006 C=0.99938 T=0.00062
GO Exome Sequencing Project European American Sub 8600 C=0.9991 T=0.0009
GO Exome Sequencing Project African American Sub 4406 C=1.0000 T=0.0000
1000Genomes Global Study-wide 5008 C=0.9970 T=0.0030
1000Genomes African Sub 1322 C=1.0000 T=0.0000
1000Genomes East Asian Sub 1008 C=0.9881 T=0.0119
1000Genomes Europe Sub 1006 C=0.9980 T=0.0020
1000Genomes South Asian Sub 978 C=0.999 T=0.001
1000Genomes American Sub 694 C=1.000 T=0.000
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.9996 T=0.0004
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.9979 T=0.0021
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.9992 T=0.0008
KOREAN population from KRGDB KOREAN Study-wide 2922 C=0.9658 T=0.0342
Korean Genome Project KOREAN Study-wide 1832 C=0.9711 T=0.0289
CNV burdens in cranial meningiomas Global Study-wide 792 C=0.985 T=0.015
CNV burdens in cranial meningiomas CRM Sub 792 C=0.985 T=0.015
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 C=0.998 T=0.002
SGDP_PRJ Global Study-wide 4 C=0.5 T=0.5
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= T
GRCh38.p13 chr 12 NC_000012.12:g.102912801= NC_000012.12:g.102912801C>T
GRCh37.p13 chr 12 NC_000012.11:g.103306579= NC_000012.11:g.103306579C>T
PAH RefSeqGene NG_008690.2:g.50610= NG_008690.2:g.50610G>A
PAH transcript variant 1 NM_000277.3:c.158= NM_000277.3:c.158G>A
PAH transcript variant 1 NM_000277.2:c.158= NM_000277.2:c.158G>A
PAH transcript NM_000277.1:c.158= NM_000277.1:c.158G>A
PAH transcript variant 2 NM_001354304.2:c.158= NM_001354304.2:c.158G>A
PAH transcript variant 2 NM_001354304.1:c.158= NM_001354304.1:c.158G>A
PAH transcript variant X1 XM_017019370.2:c.158= XM_017019370.2:c.158G>A
phenylalanine-4-hydroxylase NP_000268.1:p.Arg53= NP_000268.1:p.Arg53His
phenylalanine-4-hydroxylase NP_001341233.1:p.Arg53= NP_001341233.1:p.Arg53His
phenylalanine-4-hydroxylase isoform X1 XP_016874859.1:p.Arg53= XP_016874859.1:p.Arg53His
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#.

63 SubSNP, 17 Frequency, 3 ClinVar submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss242599067 Jul 15, 2010 (132)
2 GMI ss281528567 May 04, 2012 (137)
3 NHLBI-ESP ss342365219 May 09, 2011 (134)
4 ILLUMINA ss481752276 May 04, 2012 (137)
5 ILLUMINA ss482956618 May 04, 2012 (137)
6 EXOME_CHIP ss491472683 May 04, 2012 (137)
7 CLINSEQ_SNP ss491671167 May 04, 2012 (137)
8 PAHDB_MCGILL ss503928881 Apr 03, 2012 (136)
9 GOLDSTEINLAB ss507881604 May 04, 2012 (137)
10 ILLUMINA ss534380312 Sep 08, 2015 (146)
11 ILLUMINA ss779108383 Sep 08, 2015 (146)
12 ILLUMINA ss780691922 Sep 08, 2015 (146)
13 ILLUMINA ss781560194 Sep 08, 2015 (146)
14 ILLUMINA ss783365697 Sep 08, 2015 (146)
15 ILLUMINA ss834572547 Sep 08, 2015 (146)
16 1000GENOMES ss1346419126 Aug 21, 2014 (142)
17 BGI ss1558276669 Apr 01, 2015 (144)
18 EVA_UK10K_ALSPAC ss1629325432 Apr 01, 2015 (144)
19 EVA_UK10K_TWINSUK ss1672319465 Apr 01, 2015 (144)
20 EVA_EXAC ss1691072817 Apr 01, 2015 (144)
21 EVA_MGP ss1711340677 Apr 01, 2015 (144)
22 ILLUMINA ss1752042975 Sep 08, 2015 (146)
23 ILLUMINA ss1917877956 Feb 12, 2016 (147)
24 ILLUMINA ss1946348021 Feb 12, 2016 (147)
25 ILLUMINA ss1959461291 Feb 12, 2016 (147)
26 AMU ss1966651544 Feb 12, 2016 (147)
27 HUMAN_LONGEVITY ss2192727094 Dec 20, 2016 (150)
28 TOPMED ss2356747204 Dec 20, 2016 (150)
29 ILLUMINA ss2633001390 Nov 08, 2017 (151)
30 GRF ss2700087957 Nov 08, 2017 (151)
31 ILLUMINA ss2710769431 Nov 08, 2017 (151)
32 GNOMAD ss2740077511 Nov 08, 2017 (151)
33 GNOMAD ss2748943745 Nov 08, 2017 (151)
34 GNOMAD ss2914557338 Nov 08, 2017 (151)
35 AFFY ss2984989074 Nov 08, 2017 (151)
36 ILLUMINA ss3021460341 Nov 08, 2017 (151)
37 TOPMED ss3180235535 Nov 08, 2017 (151)
38 ILLUMINA ss3626955033 Oct 12, 2018 (152)
39 ILLUMINA ss3626955034 Oct 12, 2018 (152)
40 ILLUMINA ss3631008229 Oct 12, 2018 (152)
41 ILLUMINA ss3634520760 Oct 12, 2018 (152)
42 ILLUMINA ss3640228093 Oct 12, 2018 (152)
43 ILLUMINA ss3644601030 Oct 12, 2018 (152)
44 ILLUMINA ss3651841915 Oct 12, 2018 (152)
45 ILLUMINA ss3653758848 Oct 12, 2018 (152)
46 EGCUT_WGS ss3677554998 Jul 13, 2019 (153)
47 ILLUMINA ss3725352081 Jul 13, 2019 (153)
48 ILLUMINA ss3744400111 Jul 13, 2019 (153)
49 ILLUMINA ss3744821565 Jul 13, 2019 (153)
50 EVA ss3750898802 Jul 13, 2019 (153)
51 PAGE_CC ss3771713059 Jul 13, 2019 (153)
52 ILLUMINA ss3772320804 Jul 13, 2019 (153)
53 KHV_HUMAN_GENOMES ss3816232384 Jul 13, 2019 (153)
54 EVA ss3824763035 Apr 27, 2020 (154)
55 EVA ss3825827482 Apr 27, 2020 (154)
56 SGDP_PRJ ss3878999400 Apr 27, 2020 (154)
57 KRGDB ss3927725385 Apr 27, 2020 (154)
58 KOGIC ss3972609883 Apr 27, 2020 (154)
59 EVA ss3984672286 Apr 26, 2021 (155)
60 TOPMED ss4930862802 Apr 26, 2021 (155)
61 TOMMO_GENOMICS ss5207916559 Apr 26, 2021 (155)
62 EVA ss5236908556 Apr 26, 2021 (155)
63 EVA ss5237517567 Apr 26, 2021 (155)
64 1000Genomes NC_000012.11 - 103306579 Oct 12, 2018 (152)
65 The Avon Longitudinal Study of Parents and Children NC_000012.11 - 103306579 Oct 12, 2018 (152)
66 Genetic variation in the Estonian population NC_000012.11 - 103306579 Oct 12, 2018 (152)
67 ExAC NC_000012.11 - 103306579 Oct 12, 2018 (152)
68 gnomAD - Genomes NC_000012.12 - 102912801 Apr 26, 2021 (155)
69 gnomAD - Exomes NC_000012.11 - 103306579 Jul 13, 2019 (153)
70 GO Exome Sequencing Project NC_000012.11 - 103306579 Oct 12, 2018 (152)
71 KOREAN population from KRGDB NC_000012.11 - 103306579 Apr 27, 2020 (154)
72 Korean Genome Project NC_000012.12 - 102912801 Apr 27, 2020 (154)
73 Medical Genome Project healthy controls from Spanish population NC_000012.11 - 103306579 Apr 27, 2020 (154)
74 The PAGE Study NC_000012.12 - 102912801 Jul 13, 2019 (153)
75 CNV burdens in cranial meningiomas NC_000012.11 - 103306579 Apr 26, 2021 (155)
76 SGDP_PRJ NC_000012.11 - 103306579 Apr 27, 2020 (154)
77 8.3KJPN NC_000012.11 - 103306579 Apr 26, 2021 (155)
78 TopMed NC_000012.12 - 102912801 Apr 26, 2021 (155)
79 UK 10K study - Twins NC_000012.11 - 103306579 Oct 12, 2018 (152)
80 ALFA NC_000012.12 - 102912801 Apr 26, 2021 (155)
81 ClinVar RCV000088842.4 Apr 26, 2021 (155)
82 ClinVar RCV000490373.10 Apr 26, 2021 (155)
83 ClinVar RCV001175359.1 Apr 26, 2021 (155)
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).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss281528567, ss482956618, ss491671167, ss507881604, ss1558276669 NC_000012.10:101830708:C:T NC_000012.12:102912800:C:T (self)
59221808, 32884205, 23293246, 1383884, 9314086, 1220471, 34902779, 456437, 221781, 31016380, 65885866, 32884205, ss242599067, ss342365219, ss481752276, ss491472683, ss534380312, ss779108383, ss780691922, ss781560194, ss783365697, ss834572547, ss1346419126, ss1629325432, ss1672319465, ss1691072817, ss1711340677, ss1752042975, ss1917877956, ss1946348021, ss1959461291, ss1966651544, ss2356747204, ss2633001390, ss2700087957, ss2710769431, ss2740077511, ss2748943745, ss2914557338, ss2984989074, ss3021460341, ss3626955033, ss3626955034, ss3631008229, ss3634520760, ss3640228093, ss3644601030, ss3651841915, ss3653758848, ss3677554998, ss3744400111, ss3744821565, ss3750898802, ss3772320804, ss3824763035, ss3825827482, ss3878999400, ss3927725385, ss3984672286, ss5207916559, ss5237517567 NC_000012.11:103306578:C:T NC_000012.12:102912800:C:T (self)
RCV000088842.4, RCV000490373.10, RCV001175359.1, 417742173, 28987884, 934528, 91607321, 146408459, 13322247722, ss503928881, ss2192727094, ss3180235535, ss3725352081, ss3771713059, ss3816232384, ss3972609883, ss4930862802, ss5236908556 NC_000012.12:102912800:C:T NC_000012.12:102912800:C:T (self)
Help

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

2 citations for rs118092776
PMID Title Author Year Journal
9452061 Identification of three novel mutations in Korean phenylketonuria patients: R53H, N207D, and Y325X. Park YS et al. 1998 Human mutation
25741868 Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Richards S et al. 2015 Genetics in medicine
Help

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.

Software version is: 2.0.1.post596+ae089ad