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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.

rs5030846

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr12:102852930 (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
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.000053 (14/264690, TOPMED)
A=0.000044 (11/251076, GnomAD_exome)
A=0.000043 (6/140202, GnomAD) (+ 5 more)
A=0.000050 (6/121162, ExAC)
A=0.00017 (17/97434, ALFA)
A=0.0003 (1/3854, ALSPAC)
A=0.0000 (0/3708, TWINSUK)
A=0.000 (0/102, Ancient Sardinia)
Clinical Significance
Reported in ClinVar
Gene : Consequence
PAH : Stop Gained
Publications
9 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 97434 G=0.99983 A=0.00017
European Sub 83248 G=0.99980 A=0.00020
African Sub 4484 G=1.0000 A=0.0000
African Others Sub 140 G=1.000 A=0.000
African American Sub 4344 G=1.0000 A=0.0000
Asian Sub 470 G=1.000 A=0.000
East Asian Sub 382 G=1.000 A=0.000
Other Asian Sub 88 G=1.00 A=0.00
Latin American 1 Sub 548 G=1.000 A=0.000
Latin American 2 Sub 888 G=1.000 A=0.000
South Asian Sub 132 G=1.000 A=0.000
Other Sub 7664 G=1.0000 A=0.0000


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 G=0.999947 A=0.000053
gnomAD - Exomes Global Study-wide 251076 G=0.999956 A=0.000044
gnomAD - Exomes European Sub 135070 G=0.999919 A=0.000081
gnomAD - Exomes Asian Sub 48990 G=1.00000 A=0.00000
gnomAD - Exomes American Sub 34568 G=1.00000 A=0.00000
gnomAD - Exomes African Sub 16256 G=1.00000 A=0.00000
gnomAD - Exomes Ashkenazi Jewish Sub 10064 G=1.00000 A=0.00000
gnomAD - Exomes Other Sub 6128 G=1.0000 A=0.0000
gnomAD - Genomes Global Study-wide 140202 G=0.999957 A=0.000043
gnomAD - Genomes European Sub 75918 G=0.99993 A=0.00007
gnomAD - Genomes African Sub 42034 G=1.00000 A=0.00000
gnomAD - Genomes American Sub 13642 G=0.99993 A=0.00007
gnomAD - Genomes Ashkenazi Jewish Sub 3324 G=1.0000 A=0.0000
gnomAD - Genomes East Asian Sub 3132 G=1.0000 A=0.0000
gnomAD - Genomes Other Sub 2152 G=1.0000 A=0.0000
ExAC Global Study-wide 121162 G=0.999950 A=0.000050
ExAC Europe Sub 73190 G=0.99992 A=0.00008
ExAC Asian Sub 25136 G=1.00000 A=0.00000
ExAC American Sub 11536 G=1.00000 A=0.00000
ExAC African Sub 10392 G=1.00000 A=0.00000
ExAC Other Sub 908 G=1.000 A=0.000
Allele Frequency Aggregator Total Global 97434 G=0.99983 A=0.00017
Allele Frequency Aggregator European Sub 83248 G=0.99980 A=0.00020
Allele Frequency Aggregator Other Sub 7664 G=1.0000 A=0.0000
Allele Frequency Aggregator African Sub 4484 G=1.0000 A=0.0000
Allele Frequency Aggregator Latin American 2 Sub 888 G=1.000 A=0.000
Allele Frequency Aggregator Latin American 1 Sub 548 G=1.000 A=0.000
Allele Frequency Aggregator Asian Sub 470 G=1.000 A=0.000
Allele Frequency Aggregator South Asian Sub 132 G=1.000 A=0.000
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.9997 A=0.0003
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=1.0000 A=0.0000
Ancient Sardinia genome-wide 1240k capture data generation and analysis Global Study-wide 102 G=1.000 A=0.000
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.p14 chr 12 NC_000012.12:g.102852930G>A
GRCh37.p13 chr 12 NC_000012.11:g.103246708G>A
PAH RefSeqGene NG_008690.2:g.110481C>T
Gene: PAH, phenylalanine hydroxylase (minus strand)
Molecule type Change Amino acid[Codon] SO Term
PAH transcript variant 1 NM_000277.3:c.727C>T R [CGA] > * [TGA] Coding Sequence Variant
phenylalanine-4-hydroxylase NP_000268.1:p.Arg243Ter R (Arg) > * (Ter) Stop Gained
PAH transcript variant 2 NM_001354304.2:c.727C>T R [CGA] > * [TGA] Coding Sequence Variant
phenylalanine-4-hydroxylase NP_001341233.1:p.Arg243Ter R (Arg) > * (Ter) Stop Gained
PAH transcript variant X1 XM_017019370.2:c. N/A Genic Downstream Transcript 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: A (allele ID: 15627 )
ClinVar Accession Disease Names Clinical Significance
RCV000000619.36 Phenylketonuria Pathogenic
RCV000078528.17 not provided Pathogenic
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 G= A
GRCh38.p14 chr 12 NC_000012.12:g.102852930= NC_000012.12:g.102852930G>A
GRCh37.p13 chr 12 NC_000012.11:g.103246708= NC_000012.11:g.103246708G>A
PAH RefSeqGene NG_008690.2:g.110481= NG_008690.2:g.110481C>T
PAH transcript variant 1 NM_000277.3:c.727= NM_000277.3:c.727C>T
PAH transcript variant 1 NM_000277.2:c.727= NM_000277.2:c.727C>T
PAH transcript NM_000277.1:c.727= NM_000277.1:c.727C>T
PAH transcript variant 2 NM_001354304.2:c.727= NM_001354304.2:c.727C>T
PAH transcript variant 2 NM_001354304.1:c.727= NM_001354304.1:c.727C>T
phenylalanine-4-hydroxylase NP_000268.1:p.Arg243= NP_000268.1:p.Arg243Ter
phenylalanine-4-hydroxylase NP_001341233.1:p.Arg243= NP_001341233.1:p.Arg243Ter
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#.

42 SubSNP, 8 Frequency, 2 ClinVar submissions
No Submitter Submission ID Date (Build)
1 HGBASE ss7986013 Mar 31, 2003 (113)
2 ILLUMINA ss161109664 Dec 01, 2009 (131)
3 OMICIA ss244239164 Aug 29, 2012 (137)
4 OMIM-CURATED-RECORDS ss252841328 Aug 10, 2010 (132)
5 ILLUMINA ss482077431 May 04, 2012 (137)
6 ILLUMINA ss483026525 Sep 08, 2015 (146)
7 ILLUMINA ss485814925 May 04, 2012 (137)
8 ILLUMINA ss485827534 May 04, 2012 (137)
9 PAHDB_MCGILL ss503928212 Apr 03, 2012 (136)
10 ILLUMINA ss537652910 Sep 08, 2015 (146)
11 ILLUMINA ss778654303 Sep 08, 2015 (146)
12 ILLUMINA ss783353305 Sep 08, 2015 (146)
13 ILLUMINA ss784304425 Sep 08, 2015 (146)
14 ILLUMINA ss832615373 Sep 08, 2015 (146)
15 ILLUMINA ss834112172 Sep 08, 2015 (146)
16 EVA_UK10K_ALSPAC ss1629324586 Apr 01, 2015 (144)
17 EVA_UK10K_TWINSUK ss1672318619 Apr 01, 2015 (144)
18 EVA_EXAC ss1691072570 Apr 01, 2015 (144)
19 ILLUMINA ss1752042945 Sep 08, 2015 (146)
20 PANG-PAH-SNP ss2137543854 Oct 12, 2018 (152)
21 HUMAN_LONGEVITY ss2192723695 Dec 20, 2016 (150)
22 ILLUMINA ss2633001320 Nov 08, 2017 (151)
23 GNOMAD ss2740077164 Nov 08, 2017 (151)
24 GNOMAD ss2748943641 Nov 08, 2017 (151)
25 GNOMAD ss2914552671 Nov 08, 2017 (151)
26 ILLUMINA ss3626954923 Oct 12, 2018 (152)
27 ILLUMINA ss3631008162 Oct 12, 2018 (152)
28 ILLUMINA ss3633032212 Oct 12, 2018 (152)
29 ILLUMINA ss3633733631 Oct 12, 2018 (152)
30 ILLUMINA ss3634520732 Oct 12, 2018 (152)
31 ILLUMINA ss3635424141 Oct 12, 2018 (152)
32 ILLUMINA ss3636206813 Oct 12, 2018 (152)
33 ILLUMINA ss3637175140 Oct 12, 2018 (152)
34 ILLUMINA ss3640228065 Oct 12, 2018 (152)
35 ILLUMINA ss3725352009 Jul 13, 2019 (153)
36 ILLUMINA ss3744821537 Jul 13, 2019 (153)
37 ILLUMINA ss3772320776 Jul 13, 2019 (153)
38 EVA ss3985610986 Apr 26, 2021 (155)
39 TOPMED ss4930848756 Apr 26, 2021 (155)
40 HUGCELL_USP ss5486661815 Oct 16, 2022 (156)
41 EVA ss5847681369 Oct 16, 2022 (156)
42 EVA ss5979402108 Oct 16, 2022 (156)
43 The Avon Longitudinal Study of Parents and Children NC_000012.11 - 103246708 Oct 12, 2018 (152)
44 ExAC NC_000012.11 - 103246708 Oct 12, 2018 (152)
45 gnomAD - Genomes NC_000012.12 - 102852930 Apr 26, 2021 (155)
46 gnomAD - Exomes NC_000012.11 - 103246708 Jul 13, 2019 (153)
47 Ancient Sardinia genome-wide 1240k capture data generation and analysis NC_000012.11 - 103246708 Apr 26, 2021 (155)
48 TopMed NC_000012.12 - 102852930 Apr 26, 2021 (155)
49 UK 10K study - Twins NC_000012.11 - 103246708 Oct 12, 2018 (152)
50 ALFA NC_000012.12 - 102852930 Apr 26, 2021 (155)
51 ClinVar RCV000000619.36 Oct 16, 2022 (156)
52 ClinVar RCV000078528.17 Oct 16, 2022 (156)
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)
rs386626635 Aug 06, 2014 (136)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss485827534 NC_000012.10:101770837:G:A NC_000012.12:102852929:G:A (self)
32883270, 1383623, 9313709, 836913, 32883270, ss482077431, ss483026525, ss485814925, ss537652910, ss778654303, ss783353305, ss784304425, ss832615373, ss834112172, ss1629324586, ss1672318619, ss1691072570, ss1752042945, ss2633001320, ss2740077164, ss2748943641, ss2914552671, ss3626954923, ss3631008162, ss3633032212, ss3633733631, ss3634520732, ss3635424141, ss3636206813, ss3637175140, ss3640228065, ss3744821537, ss3772320776, ss3985610986, ss5847681369, ss5979402108 NC_000012.11:103246707:G:A NC_000012.12:102852929:G:A (self)
RCV000000619.36, RCV000078528.17, 417729968, 146394413, 3142421707, ss244239164, ss252841328, ss503928212, ss2137543854, ss2192723695, ss3725352009, ss4930848756, ss5486661815 NC_000012.12:102852929:G:A NC_000012.12:102852929:G:A (self)
ss7986013, ss161109664 NT_029419.12:65390013:G:A NC_000012.12:102852929:G:A (self)
Help

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

9 citations for rs5030846
PMID Title Author Year Journal
2006152 Founder effect of a prevalent phenylketonuria mutation in the Oriental population. Wang T et al. 1991 Proceedings of the National Academy of Sciences of the United States of America
2309142 Molecular genetics of PKU in eastern Europe: a nonsense mutation associated with haplotype 4 of the phenylalanine hydroxylase gene. Wang T et al. 1990 Somatic cell and molecular genetics
8320703 Comparison of genotype and intellectual phenotype in untreated PKU patients. Ramus SJ et al. 1993 Journal of medical genetics
11486900 Tetrahydrobiopterin-responsive phenylalanine hydroxylase deficiency in Dutch neonates. Spaapen LJ et al. 2001 Journal of inherited metabolic disease
17935162 Molecular genetics of tetrahydrobiopterin-responsive phenylalanine hydroxylase deficiency. Zurflüh MR et al. 2008 Human mutation
20920871 Mutation spectrum of phenylketonuria in Iranian population. Zare-Karizi Sh et al. 2011 Molecular genetics and metabolism
23500595 Molecular epidemiology and BH4-responsiveness in patients with phenylalanine hydroxylase deficiency from Galicia region of Spain. Couce ML et al. 2013 Gene
23757202 Free the data: one laboratory's approach to knowledge-based genomic variant classification and preparation for EMR integration of genomic data. Bean LJ et al. 2013 Human mutation
24130151 Splice, insertion-deletion and nonsense mutations that perturb the phenylalanine hydroxylase transcript cause phenylketonuria in India. Bashyam MD et al. 2014 Journal of cellular biochemistry
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.post761+d5e8e07