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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.


Current Build 155

Released April 9, 2021

Homo sapiens
chr3:120675864 (GRCh38.p13) 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.

Variation Type
SNV Single Nucleotide Variation
T=0.000030 (8/264690, TOPMED)
T=0.000020 (5/251028, GnomAD_exome)
T=0.000043 (6/140250, GnomAD) (+ 2 more)
T=0.000025 (3/121270, ExAC)
T=0.00007 (3/44872, ALFA)
Clinical Significance
Reported in ClinVar
Gene : Consequence
HGD : Splice Acceptor Variant
2 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: 20201027095038
Population Group Sample Size Ref Allele Alt Allele
Total Global 44872 C=0.99993 T=0.00007
European Sub 32630 C=0.99991 T=0.00009
African Sub 3938 C=1.0000 T=0.0000
African Others Sub 122 C=1.000 T=0.000
African American Sub 3816 C=1.0000 T=0.0000
Asian Sub 168 C=1.000 T=0.000
East Asian Sub 112 C=1.000 T=0.000
Other Asian Sub 56 C=1.00 T=0.00
Latin American 1 Sub 500 C=1.000 T=0.000
Latin American 2 Sub 628 C=1.000 T=0.000
South Asian Sub 98 C=1.00 T=0.00
Other Sub 6910 C=1.0000 T=0.0000


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").

Study Population Group Sample Size Ref Allele Alt Allele
TopMed Global Study-wide 264690 C=0.999970 T=0.000030
gnomAD - Exomes Global Study-wide 251028 C=0.999980 T=0.000020
gnomAD - Exomes European Sub 135062 C=0.999963 T=0.000037
gnomAD - Exomes Asian Sub 48990 C=1.00000 T=0.00000
gnomAD - Exomes American Sub 34538 C=1.00000 T=0.00000
gnomAD - Exomes African Sub 16250 C=1.00000 T=0.00000
gnomAD - Exomes Ashkenazi Jewish Sub 10066 C=1.00000 T=0.00000
gnomAD - Exomes Other Sub 6122 C=1.0000 T=0.0000
gnomAD - Genomes Global Study-wide 140250 C=0.999957 T=0.000043
gnomAD - Genomes European Sub 75962 C=0.99992 T=0.00008
gnomAD - Genomes African Sub 42032 C=1.00000 T=0.00000
gnomAD - Genomes American Sub 13656 C=1.00000 T=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3322 C=1.0000 T=0.0000
gnomAD - Genomes East Asian Sub 3128 C=1.0000 T=0.0000
gnomAD - Genomes Other Sub 2150 C=1.0000 T=0.0000
ExAC Global Study-wide 121270 C=0.999975 T=0.000025
ExAC Europe Sub 73316 C=0.99996 T=0.00004
ExAC Asian Sub 25134 C=1.00000 T=0.00000
ExAC American Sub 11506 C=1.00000 T=0.00000
ExAC African Sub 10406 C=1.00000 T=0.00000
ExAC Other Sub 908 C=1.000 T=0.000

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.p13 chr 3 NC_000003.12:g.120675864C>T
GRCh37.p13 chr 3 NC_000003.11:g.120394711C>T
HGD RefSeqGene NG_011957.1:g.11618G>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 Acceptor Variant
HGD transcript variant X1 XM_005247412.2:c. N/A Splice Acceptor Variant
HGD transcript variant X2 XM_005247413.2:c. N/A Splice Acceptor Variant
HGD transcript variant X5 XM_005247414.5:c. N/A Splice Acceptor Variant
HGD transcript variant X4 XM_011512746.2:c. N/A Splice Acceptor Variant
HGD transcript variant X3 XM_017006277.2:c. N/A Splice Acceptor Variant

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: 18209 )
ClinVar Accession Disease Names Clinical Significance
RCV000003320.5 Alkaptonuria Pathogenic

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
GRCh38.p13 chr 3 NC_000003.12:g.120675864= NC_000003.12:g.120675864C>T
GRCh37.p13 chr 3 NC_000003.11:g.120394711= NC_000003.11:g.120394711C>T
HGD RefSeqGene NG_011957.1:g.11618= NG_011957.1:g.11618G>A

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#.

8 SubSNP, 5 Frequency, 1 ClinVar submissions
No Submitter Submission ID Date (Build)
1 OMIM-CURATED-RECORDS ss836188708 Oct 23, 2013 (136)
2 EVA_EXAC ss1687158615 Apr 01, 2015 (144)
3 HUMAN_LONGEVITY ss2255255129 Dec 20, 2016 (150)
4 GNOMAD ss2733990759 Nov 08, 2017 (151)
5 TOPMED ss3403603774 Nov 08, 2017 (151)
6 ILLUMINA ss3726050117 Jul 13, 2019 (153)
7 GNOMAD ss4079539234 Apr 26, 2021 (155)
8 TOPMED ss4581098815 Apr 26, 2021 (155)
9 ExAC NC_000003.11 - 120394711 Oct 12, 2018 (152)
10 gnomAD - Genomes NC_000003.12 - 120675864 Apr 26, 2021 (155)
11 gnomAD - Exomes NC_000003.11 - 120394711 Jul 13, 2019 (153)
12 TopMed NC_000003.12 - 120675864 Apr 26, 2021 (155)
13 ALFA NC_000003.12 - 120675864 Apr 26, 2021 (155)
14 ClinVar RCV000003320.5 Apr 26, 2021 (155)

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
7094551, 3076263, ss1687158615, ss2733990759 NC_000003.11:120394710:C:T NC_000003.12:120675863:C:T (self)
RCV000003320.5, 121671663, 261525032, 418476370, 5233356389, ss836188708, ss2255255129, ss3403603774, ss3726050117, ss4079539234, ss4581098815 NC_000003.12:120675863:C:T NC_000003.12:120675863:C:T (self)

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

2 citations for rs397515347
PMID Title Author Year Journal
10482952 Allelic heterogeneity of alkaptonuria in Central Europe. Müller CR et al. 1999 European journal of human genetics
20301627 Alkaptonuria Introne WJ et al. 1993 GeneReviews®

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.post629+eb05767