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dbSNP Short Genetic Variations

Reference SNP (rs) Report

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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.

rs62507348

Current Build 151

Released July 17, 2018

Organism
Homo sapiens
Position
chr12:102855148 (GRCh38.p7) 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 (1/246062, GnomAD)
A=0.00002 (2/125568, TOPMED)
A=0.00001 (1/121362, ExAC) (+ 1 more)
A=0.0002 (2/13006, GO-ESP)
Clinical Significance
Reported in ClinVar
Gene : Consequence
PAH : Stop Gained
Publications
4 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.p7 chr 12 NC_000012.12:g.102855148G>A
GRCh37.p13 chr 12 NC_000012.11:g.103248926G>A
PAH RefSeqGene NG_008690.1:g.67455C>T
Gene: PAH, phenylalanine hydroxylase (minus strand)
Molecule type Change Amino acid[Codon] SO Term
PAH transcript NM_000277.1:c.694C>T Q [CAA] > * [TAA] Coding Sequence Variant
phenylalanine-4-hydroxylase NP_000268.1:p.Gln...

NP_000268.1:p.Gln232Ter

Q (Gln) > * (Ter) Stop Gained
PAH transcript variant X1 XM_017019370.1:c....

XM_017019370.1:c.694C>T

Q [CAG] > * [TAG] Coding Sequence Variant
phenylalanine-4-hydroxylase isoform X1 XP_016874859.1:p....

XP_016874859.1:p.Gln232Ter

Q (Gln) > * (Ter) Stop Gained
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: 108524 )
ClinVar Accession Disease Names Clinical Significance
RCV000089039.1 not provided Pathogenic
RCV000169464.1 Phenylketonuria Likely-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").

Download
Study Population Group Sample Size Ref Allele Alt Allele
Trans-Omics for Precision Medicine Global Study-wide 125568 G=0.99998 A=0.00002
The Exome Aggregation Consortium Global Study-wide 121362 G=0.99999 A=0.00001
The Exome Aggregation Consortium Europe Sub 73336 G=1.0000 A=0.0000
The Exome Aggregation Consortium Asian Sub 25144 G=1.0000 A=0.0000
The Exome Aggregation Consortium American Sub 11568 G=1.0000 A=0.0000
The Exome Aggregation Consortium African Sub 10406 G=0.9999 A=0.0001
The Exome Aggregation Consortium Other Sub 908 G=1.00 A=0.00
GO Exome Sequencing Project Global Study-wide 13006 G=0.9998 A=0.0002
GO Exome Sequencing Project European American Sub 8600 G=1.000 A=0.000
GO Exome Sequencing Project African American Sub 4406 G=1.000 A=0.000
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.p7 chr 12 NC_000012.12:g.102855148G= NC_000012.12:g.10285514...

NC_000012.12:g.102855148G>A

GRCh37.p13 chr 12 NC_000012.11:g.103248926G= NC_000012.11:g.10324892...

NC_000012.11:g.103248926G>A

PAH RefSeqGene NG_008690.1:g.67455C= NG_008690.1:g.67455C>T
PAH transcript NM_000277.1:c.694C= NM_000277.1:c.694C>T
PAH transcript variant X1 XM_017019370.1:c.694C= XM_017019370.1:c.694C>T
phenylalanine-4-hydroxylase NP_000268.1:p.Gln232= NP_000268.1:p.Gln232Ter
phenylalanine-4-hydroxylase isoform X1 XP_016874859.1:p.Gln232= XP_016874859.1:p.Gln232Ter
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#.

2 ClinVar, 4 Frequency, 12 SubSNP submissions
No Submitter Submission ID Date (Build)
1 PAHDB_MCGILL ss503928933 Apr 03, 2012 (136)
2 NHLBI-ESP ss713120864 Apr 25, 2013 (138)
3 EVA_EXAC ss1691072609 Apr 01, 2015 (144)
4 ILLUMINA ss1946348000 Feb 12, 2016 (147)
5 ILLUMINA ss1959461247 Feb 12, 2016 (147)
6 TOPMED ss2356743869 Dec 20, 2016 (150)
7 GNOMAD ss2740077221 Nov 08, 2017 (151)
8 AFFY ss2984989048 Nov 08, 2017 (151)
9 ILLUMINA ss3021460268 Nov 08, 2017 (151)
10 TOPMED ss3180224931 Nov 08, 2017 (151)
11 ILLUMINA ss3625632061 Jul 20, 2018 (151)
12 ILLUMINA ss3644601009 Jul 20, 2018 (151)
13 The Exome Aggregation Consortium NC_000012.11 - 103248926 Jul 20, 2018 (151)
14 The Genome Aggregation Database NC_000012.11 - 103248926 Jul 20, 2018 (151)
15 GO Exome Sequencing Project NC_000012.11 - 103248926 Jul 20, 2018 (151)
16 Trans-Omics for Precision Medicine NC_000012.12 - 102855148 Jul 20, 2018 (151)
17 ClinVar RCV000089039.1 Jul 20, 2018 (151)
18 ClinVar RCV000169464.1 Jul 20, 2018 (151)
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
1383663, 9091956, 1220419, ss713120864, ss1691072609, ss1946348000, ss1959461247, ss2356743869, ss2740077221, ss2984989048, ss3021460268, ss3625632061, ss3644601009 NC_000012.11:103248925:G= NC_000012.12:102855147:G= (self)
91598920, ss503928933, ss3180224931 NC_000012.12:102855147:G= NC_000012.12:102855147:G= (self)
1383663, 9091956, 1220419, ss713120864, ss1691072609, ss1946348000, ss1959461247, ss2356743869, ss2740077221, ss2984989048, ss3021460268, ss3625632061, ss3644601009 NC_000012.11:103248925:G>A NC_000012.12:102855147:G>A (self)
RCV000089039.1, RCV000169464.1, 91598920, ss503928933, ss3180224931 NC_000012.12:102855147:G>A NC_000012.12:102855147: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.

4 citations for rs62507348
PMID Title Author Year Journal
10408782 Molecular characterization of phenylalanine hydroxylase deficiency in Chile. Mutations in brief no. 243. Online. PĂ©rez B et al. 1999 Human mutation
16256386 Phenylketonuria mutations in Northern China. Song F et al. 2005 Molecular genetics and metabolism
23932990 Variations in genotype-phenotype correlations in phenylalanine hydroxylase deficiency in Chinese Han population. Zhu T et al. 2013 Gene
24510552 [Analysis for phenylalanine hydroxylase gene mutations in 35 ethnic Hui children from Ningxia with phenylketonuria]. Mao X et al. 2014 Zhonghua yi xue yi chuan xue za zhi = Zhonghua yixue yichuanxue zazhi = Chinese journal of medical genetics

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: 0.1.4.post833+d3ba21e