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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.

rs397515518

Current Build 154

Released April 21, 2020

Organism
Homo sapiens
Position
chr3:120652591 (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>A / C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.000016 (4/250876, GnomAD_exome)
T=0.000016 (2/125568, TOPMED)
A=0.000025 (3/120428, ExAC) (+ 1 more)
A=0.00009 (1/11176, ALFA Project)
Clinical Significance
Reported in ClinVar
Gene : Consequence
HGD : Splice Donor Variant
Publications
6 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 3 NC_000003.12:g.120652591C>A
GRCh38.p12 chr 3 NC_000003.12:g.120652591C>T
GRCh37.p13 chr 3 NC_000003.11:g.120371438C>A
GRCh37.p13 chr 3 NC_000003.11:g.120371438C>T
HGD RefSeqGene NG_011957.1:g.34891G>T
HGD RefSeqGene NG_011957.1:g.34891G>A
Gene: HGD, homogentisate 1,2-dioxygenase (minus strand)
Molecule type Change Amino acid[Codon] SO Term
HGD transcript NM_000187.4:c. N/A Splice Donor Variant
HGD transcript variant X1 XM_005247412.2:c. N/A Splice Donor Variant
HGD transcript variant X2 XM_005247413.2:c. N/A Splice Donor Variant
HGD transcript variant X5 XM_005247414.5:c. N/A Splice Donor Variant
HGD transcript variant X4 XM_011512746.2:c. N/A Splice Donor Variant
HGD transcript variant X3 XM_017006277.2:c. N/A Splice Donor 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: 186673 )
ClinVar Accession Disease Names Clinical Significance
RCV000169542.1 Alkaptonuria Likely-Pathogenic
Allele: T (allele ID: 76485 )
ClinVar Accession Disease Names Clinical Significance
RCV000055781.2 Alkaptonuria Likely-Pathogenic

ALFA Allele Frequency (New)
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 23038 C=0.99996 A=0.00004, T=0.00000
European Sub 15752 C=0.99994 A=0.00006, T=0.00000
African Sub 3492 C=1.0000 A=0.0000, T=0.0000
African Others Sub 122 C=1.000 A=0.000, T=0.000
African American Sub 3370 C=1.0000 A=0.0000, T=0.0000
Asian Sub 168 C=1.000 A=0.000, T=0.000
East Asian Sub 112 C=1.000 A=0.000, T=0.000
Other Asian Sub 56 C=1.00 A=0.00, T=0.00
Latin American 1 Sub 146 C=1.000 A=0.000, T=0.000
Latin American 2 Sub 610 C=1.000 A=0.000, T=0.000
South Asian Sub 98 C=1.00 A=0.00, T=0.00
Other Sub 2772 C=1.0000 A=0.0000, T=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
gnomAD - Exomes Global Study-wide 250876 C=0.999984 A=0.000016
gnomAD - Exomes European Sub 134948 C=0.999978 A=0.000022
gnomAD - Exomes Asian Sub 48930 C=0.99998 A=0.00002
gnomAD - Exomes American Sub 34566 C=1.00000 A=0.00000
gnomAD - Exomes African Sub 16254 C=1.00000 A=0.00000
gnomAD - Exomes Ashkenazi Jewish Sub 10058 C=1.00000 A=0.00000
gnomAD - Exomes Other Sub 6120 C=1.0000 A=0.0000
TopMed Global Study-wide 125568 C=0.999976 A=0.000008, T=0.000016
ExAC Global Study-wide 120428 C=0.999975 A=0.000025
ExAC Europe Sub 72774 C=0.99996 A=0.00004
ExAC Asian Sub 24886 C=1.00000 A=0.00000
ExAC American Sub 11492 C=1.00000 A=0.00000
ExAC African Sub 10380 C=1.00000 A=0.00000
ExAC Other Sub 896 C=1.000 A=0.000
ALFA Total Global 11176 C=0.99991 A=0.00009, T=0.00000
ALFA European Sub 8134 C=0.9999 A=0.0001, T=0.0000
ALFA Other Sub 2302 C=1.0000 A=0.0000, T=0.0000
ALFA African Sub 676 C=1.000 A=0.000, T=0.000
ALFA Asian Sub 60 C=1.00 A=0.00, T=0.00
ALFA South Asian Sub 4 C=1.0 A=0.0, T=0.0
ALFA Latin American 1 Sub 0 C=0 A=0, T=0
ALFA Latin American 2 Sub 0 C=0 A=0, T=0
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= A T
GRCh38.p12 chr 3 NC_000003.12:g.120652591= NC_000003.12:g.120652591C>A NC_000003.12:g.120652591C>T
GRCh37.p13 chr 3 NC_000003.11:g.120371438= NC_000003.11:g.120371438C>A NC_000003.11:g.120371438C>T
HGD RefSeqGene NG_011957.1:g.34891= NG_011957.1:g.34891G>T NG_011957.1:g.34891G>A
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#.

6 SubSNP, 4 Frequency, 2 ClinVar submissions
No Submitter Submission ID Date (Build)
1 CLINVAR ss836189083 Oct 23, 2013 (136)
2 EVA_EXAC ss1687158490 Apr 01, 2015 (144)
3 CLINVAR ss1751114103 May 21, 2015 (144)
4 GNOMAD ss2733990585 Nov 08, 2017 (151)
5 TOPMED ss3403599697 Nov 08, 2017 (151)
6 TOPMED ss3403599698 Nov 08, 2017 (151)
7 ExAC NC_000003.11 - 120371438 Oct 12, 2018 (152)
8 gnomAD - Exomes NC_000003.11 - 120371438 Jul 13, 2019 (153)
9 TopMed NC_000003.12 - 120652591 Oct 12, 2018 (152)
10 dbGaP Population Frequency Project NC_000003.12 - 120652591 Apr 25, 2020 (154)
11 ClinVar RCV000055781.2 Oct 12, 2018 (152)
12 ClinVar RCV000169542.1 Oct 12, 2018 (152)
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
7094421, 3076082, ss1687158490, ss2733990585 NC_000003.11:120371437:C:A NC_000003.12:120652590:C:A (self)
RCV000169542.1, 261521588, 596723445, ss1751114103, ss3403599697 NC_000003.12:120652590:C:A NC_000003.12:120652590:C:A (self)
ss2733990585 NC_000003.11:120371437:C:T NC_000003.12:120652590:C:T (self)
RCV000055781.2, 261521588, 596723445, ss836189083, ss3403599698 NC_000003.12:120652590:C:T NC_000003.12:120652590: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.

6 citations for rs397515518
PMID Title Author Year Journal
9529363 Mutation and polymorphism analysis of the human homogentisate 1, 2-dioxygenase gene in alkaptonuria patients. Beltrán-Valero de Bernabé D et al. 1998 American journal of human genetics
11017803 High frequency of alkaptonuria in Slovakia: evidence for the appearance of multiple mutations in HGO involving different mutational hot spots. Zatková A et al. 2000 American journal of human genetics
12501223 Natural history of alkaptonuria. Phornphutkul C et al. 2002 The New England journal of medicine
19862842 Mutation spectrum of homogentisic acid oxidase (HGD) in alkaptonuria. Vilboux T et al. 2009 Human mutation
20301627 Alkaptonuria Introne WJ et al. 1993 GeneReviews®
21720873 An update on molecular genetics of Alkaptonuria (AKU). Zatkova A et al. 2011 Journal of inherited metabolic disease
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.post557+f76c771