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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 Aliases 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 153

Released July 9, 2019

Organism
Homo sapiens
Position
chr12:102912801 (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>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.00168 (422/251382, GnomAD_exome)
T=0.00190 (238/125568, TOPMED)
T=0.00175 (212/121382, ExAC) (+ 7 more)
T=0.0049 (387/78702, PAGE_STUDY)
T=0.0011 (33/31402, GnomAD)
T=0.0006 (8/13006, GO-ESP)
T=0.003 (15/5008, 1000G)
T=0.000 (2/4480, Estonian)
T=0.002 (8/3854, ALSPAC)
T=0.001 (3/3708, TWINSUK)
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.p12 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
RCV000088842.1 not provided Uncertain-Significance
RCV000490373.5 Phenylketonuria Uncertain-Significance
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
gnomAD - Exomes Global Study-wide 251382 C=0.99832 T=0.00168
gnomAD - Exomes European Sub 135316 C=0.99942 T=0.00058
gnomAD - Exomes Asian Sub 49006 C=0.9939 T=0.0061
gnomAD - Exomes American Sub 34590 C=0.9990 T=0.0010
gnomAD - Exomes African Sub 16256 C=0.9998 T=0.0002
gnomAD - Exomes Ashkenazi Jewish Sub 10078 C=0.9999 T=0.0001
gnomAD - Exomes Other Sub 6136 C=0.999 T=0.001
TopMed Global Study-wide 125568 C=0.99810 T=0.00190
ExAC Global Study-wide 121382 C=0.99825 T=0.00175
ExAC Europe Sub 73336 C=0.9994 T=0.0006
ExAC Asian Sub 25156 C=0.9936 T=0.0064
ExAC American Sub 11578 C=0.9997 T=0.0003
ExAC African Sub 10404 C=0.9999 T=0.0001
ExAC Other Sub 908 C=1.00 T=0.00
The PAGE Study Global Study-wide 78702 C=0.9951 T=0.0049
The PAGE Study AfricanAmerican Sub 32516 C=0.9998 T=0.0002
The PAGE Study Mexican Sub 10810 C=0.9993 T=0.0007
The PAGE Study Asian Sub 8318 C=0.960 T=0.040
The PAGE Study PuertoRican Sub 7918 C=1.000 T=0.000
The PAGE Study NativeHawaiian Sub 4534 C=0.996 T=0.004
The PAGE Study Cuban Sub 4230 C=0.999 T=0.001
The PAGE Study Dominican Sub 3828 C=0.998 T=0.002
The PAGE Study CentralAmerican Sub 2450 C=0.999 T=0.001
The PAGE Study SouthAmerican Sub 1982 C=0.998 T=0.002
The PAGE Study NativeAmerican Sub 1260 C=0.998 T=0.002
The PAGE Study SouthAsian Sub 856 C=1.00 T=0.00
gnomAD - Genomes Global Study-wide 31402 C=0.9989 T=0.0011
gnomAD - Genomes European Sub 18908 C=0.9995 T=0.0005
gnomAD - Genomes African Sub 8710 C=1.000 T=0.000
gnomAD - Genomes East Asian Sub 1558 C=0.987 T=0.013
gnomAD - Genomes Other Sub 1088 C=1.000 T=0.000
gnomAD - Genomes American Sub 848 C=1.00 T=0.00
gnomAD - Genomes Ashkenazi Jewish Sub 290 C=1.00 T=0.00
GO Exome Sequencing Project Global Study-wide 13006 C=0.9994 T=0.0006
GO Exome Sequencing Project European American Sub 8600 C=0.999 T=0.001
GO Exome Sequencing Project African American Sub 4406 C=1.000 T=0.000
1000Genomes Global Study-wide 5008 C=0.997 T=0.003
1000Genomes African Sub 1322 C=1.000 T=0.000
1000Genomes East Asian Sub 1008 C=0.988 T=0.012
1000Genomes Europe Sub 1006 C=0.998 T=0.002
1000Genomes South Asian Sub 978 C=1.00 T=0.00
1000Genomes American Sub 694 C=1.00 T=0.00
Genetic variation in the Estonian population Estonian Study-wide 4480 C=1.000 T=0.000
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.998 T=0.002
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.999 T=0.001
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 Note
GRCh38.p12 chr 12 NC_000012.12:g.102912801= NC_000012.12:g.10291280...

NC_000012.12:g.102912801C>T

GRCh37.p13 chr 12 NC_000012.11:g.103306579= NC_000012.11:g.10330657...

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_001354304.1:c.158= NM_001354304.1:c.158G>A
PAH transcript variant 2 NM_001354304.2:c.158= NM_001354304.2: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#.

53 SubSNP, 10 Frequency, 2 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 1000Genomes NC_000012.11 - 103306579 Oct 12, 2018 (152)
55 The Avon Longitudinal Study of Parents and Children NC_000012.11 - 103306579 Oct 12, 2018 (152)
56 Genetic variation in the Estonian population NC_000012.11 - 103306579 Oct 12, 2018 (152)
57 ExAC NC_000012.11 - 103306579 Oct 12, 2018 (152)
58 gnomAD - Genomes NC_000012.11 - 103306579 Jul 13, 2019 (153)
59 gnomAD - Exomes NC_000012.11 - 103306579 Jul 13, 2019 (153)
60 GO Exome Sequencing Project NC_000012.11 - 103306579 Oct 12, 2018 (152)
61 The PAGE Study NC_000012.12 - 102912801 Jul 13, 2019 (153)
62 TopMed NC_000012.12 - 102912801 Oct 12, 2018 (152)
63 UK 10K study - Twins NC_000012.11 - 103306579 Oct 12, 2018 (152)
64 ClinVar RCV000088842.1 Oct 12, 2018 (152)
65 ClinVar RCV000490373.5 Jul 13, 2019 (153)
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, 161686974, 9314086, 1220471, 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 NC_000012.11:103306578:C:T NC_000012.12:102912800:C:T (self)
RCV000088842.1, RCV000490373.5, 934528, 91607321, ss503928881, ss2192727094, ss3180235535, ss3725352081, ss3771713059, ss3816232384 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

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.post308+0fe9b3b