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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.

rs104894280

Current Build 153

Released July 9, 2019

Organism
Homo sapiens
Position
chr11:112233205 (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
G>A
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.00000 (1/251410, GnomAD_exome)
A=0.00003 (4/125568, TOPMED)
A=0.0000 (3/78696, PAGE_STUDY) (+ 1 more)
A=0.000 (1/5008, 1000G)
Clinical Significance
Reported in ClinVar
Gene : Consequence
PTS : Missense Variant
Publications
1 citation
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 11 NC_000011.10:g.112233205G>A
GRCh37.p13 chr 11 NC_000011.9:g.112103928G>A
PTS RefSeqGene NG_008743.1:g.11841G>A
Gene: PTS, 6-pyruvoyltetrahydropterin synthase (plus strand)
Molecule type Change Amino acid[Codon] SO Term
PTS transcript NM_000317.3:c.286G>A D [GAT] > N [AAT] Coding Sequence Variant
6-pyruvoyl tetrahydrobiopterin synthase NP_000308.1:p.Asp96Asn D (Asp) > N (Asn) 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: A (allele ID: 15523 )
ClinVar Accession Disease Names Clinical Significance
RCV000000513.4 6-pyruvoyl-tetrahydropterin synthase deficiency Pathogenic
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").

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Study Population Group Sample Size Ref Allele Alt Allele
gnomAD - Exomes Global Study-wide 251410 G=1.00000 A=0.00000
gnomAD - Exomes European Sub 135342 G=1.00000 A=0.00000
gnomAD - Exomes Asian Sub 49008 G=1.0000 A=0.0000
gnomAD - Exomes American Sub 34592 G=1.0000 A=0.0000
gnomAD - Exomes African Sub 16256 G=1.0000 A=0.0000
gnomAD - Exomes Ashkenazi Jewish Sub 10076 G=1.0000 A=0.0000
gnomAD - Exomes Other Sub 6136 G=1.000 A=0.000
TopMed Global Study-wide 125568 G=0.99997 A=0.00003
The PAGE Study Global Study-wide 78696 G=1.0000 A=0.0000
The PAGE Study AfricanAmerican Sub 32516 G=1.0000 A=0.0000
The PAGE Study Mexican Sub 10808 G=1.0000 A=0.0000
The PAGE Study Asian Sub 8318 G=1.000 A=0.000
The PAGE Study PuertoRican Sub 7918 G=1.000 A=0.000
The PAGE Study NativeHawaiian Sub 4532 G=1.000 A=0.000
The PAGE Study Cuban Sub 4230 G=1.000 A=0.000
The PAGE Study Dominican Sub 3826 G=1.000 A=0.000
The PAGE Study CentralAmerican Sub 2450 G=1.000 A=0.000
The PAGE Study SouthAmerican Sub 1982 G=1.000 A=0.000
The PAGE Study NativeAmerican Sub 1260 G=1.000 A=0.000
The PAGE Study SouthAsian Sub 856 G=1.00 A=0.00
1000Genomes Global Study-wide 5008 G=1.000 A=0.000
1000Genomes African Sub 1322 G=1.000 A=0.000
1000Genomes East Asian Sub 1008 G=0.999 A=0.001
1000Genomes Europe Sub 1006 G=1.000 A=0.000
1000Genomes South Asian Sub 978 G=1.00 A=0.00
1000Genomes American Sub 694 G=1.00 A=0.00
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 Note
GRCh38.p12 chr 11 NC_000011.10:g.112233205= NC_000011.10:g.11223320...

NC_000011.10:g.112233205G>A

GRCh37.p13 chr 11 NC_000011.9:g.112103928= NC_000011.9:g.112103928G>A
PTS RefSeqGene NG_008743.1:g.11841= NG_008743.1:g.11841G>A
PTS transcript NM_000317.3:c.286= NM_000317.3:c.286G>A
PTS transcript NM_000317.2:c.286= NM_000317.2:c.286G>A
6-pyruvoyl tetrahydrobiopterin synthase NP_000308.1:p.Asp96= NP_000308.1:p.Asp96Asn
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#.

11 SubSNP, 4 Frequency, 1 ClinVar submissions
No Submitter Submission ID Date (Build)
1 OMICIA ss244239008 May 28, 2010 (132)
2 OMIM-CURATED-RECORDS ss252444680 Jul 15, 2010 (132)
3 1000GENOMES ss488976225 May 04, 2012 (137)
4 1000GENOMES ss1342990479 Aug 21, 2014 (142)
5 ILLUMINA ss1959385875 Feb 12, 2016 (147)
6 ILLUMINA ss3021376491 Nov 08, 2017 (151)
7 TOPMED ss3156566612 Nov 08, 2017 (151)
8 ILLUMINA ss3651743990 Oct 12, 2018 (152)
9 ILLUMINA ss3725276780 Jul 13, 2019 (153)
10 EVA ss3749818743 Jul 13, 2019 (153)
11 PAGE_CC ss3771652844 Jul 13, 2019 (153)
12 1000Genomes NC_000011.9 - 112103928 Oct 12, 2018 (152)
13 gnomAD - Exomes NC_000011.9 - 112103928 Jul 13, 2019 (153)
14 The PAGE Study NC_000011.10 - 112233205 Jul 13, 2019 (153)
15 TopMed NC_000011.10 - 112233205 Oct 12, 2018 (152)
16 ClinVar RCV000000513.4 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).

Associated ID History Updated (Build)
rs118192112 Oct 26, 2010 (133)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
55573799, 8609610, ss488976225, ss1342990479, ss1959385875, ss3021376491, ss3651743990, ss3749818743 NC_000011.9:112103927:G:A NC_000011.10:112233204:G:A (self)
RCV000000513.4, 874313, 72568771, ss244239008, ss252444680, ss3156566612, ss3725276780, ss3771652844 NC_000011.10:112233204:G:A NC_000011.10:112233204: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.

1 citation for rs104894280
PMID Title Author Year Journal
9450907 Mutation analysis of the 6-pyruvoyl-tetrahydropterin synthase gene in Chinese hyperphenylalaninemia caused by tetrahydrobiopterin synthesis deficiency. Liu TT et al. 1998 Human mutation

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.post270+ab078da