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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.


Current Build 153

Released July 9, 2019

Homo sapiens
chr3:120670449 (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.

Variation Type
SNV Single Nucleotide Variation
G=0.00084 (210/251280, GnomAD_exome)
G=0.00436 (548/125568, TOPMED)
G=0.00109 (132/121268, ExAC) (+ 4 more)
G=0.0061 (477/78702, PAGE_STUDY)
G=0.0035 (109/31400, GnomAD)
G=0.0039 (51/12998, GO-ESP)
G=0.003 (16/5008, 1000G)
Clinical Significance
Reported in ClinVar
Gene : Consequence
HGD : Missense Variant
1 citation
Genomic View
See rs on genome

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.120670449T>G
GRCh37.p13 chr 3 NC_000003.11:g.120389296T>G
HGD RefSeqGene NG_011957.1:g.17033A>C
Gene: HGD, homogentisate 1,2-dioxygenase (minus strand)
Molecule type Change Amino acid[Codon] SO Term
HGD transcript NM_000187.4:c.260A>C E [GAA] > A [GCA] Coding Sequence Variant
homogentisate 1,2-dioxygenase NP_000178.2:p.Glu87Ala E (Glu) > A (Ala) Missense Variant
HGD transcript variant X3 XM_017006277.2:c. N/A 5 Prime UTR Variant
HGD transcript variant X1 XM_005247412.2:c.260A>C E [GAA] > A [GCA] Coding Sequence Variant
homogentisate 1,2-dioxygenase isoform X1 XP_005247469.1:p.Glu87Ala E (Glu) > A (Ala) Missense Variant
HGD transcript variant X2 XM_005247413.2:c.260A>C E [GAA] > A [GCA] Coding Sequence Variant
homogentisate 1,2-dioxygenase isoform X2 XP_005247470.1:p.Glu87Ala E (Glu) > A (Ala) Missense Variant
HGD transcript variant X4 XM_011512746.2:c.260A>C E [GAA] > A [GCA] Coding Sequence Variant
homogentisate 1,2-dioxygenase isoform X4 XP_011511048.1:p.Glu87Ala E (Glu) > A (Ala) Missense Variant
HGD transcript variant X5 XM_005247414.5:c.260A>C E [GAA] > A [GCA] Coding Sequence Variant
homogentisate 1,2-dioxygenase isoform X5 XP_005247471.1:p.Glu87Ala E (Glu) > A (Ala) Missense 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: G (allele ID: 289025 )
ClinVar Accession Disease Names Clinical Significance
RCV000400316.1 Alkaptonuria Uncertain-Significance

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
gnomAD - Exomes Global Study-wide 251280 T=0.99916 G=0.00084
gnomAD - Exomes European Sub 135290 T=1.00000 G=0.00000
gnomAD - Exomes Asian Sub 48998 T=0.9999 G=0.0001
gnomAD - Exomes American Sub 34534 T=0.9996 G=0.0004
gnomAD - Exomes African Sub 16252 T=0.9882 G=0.0118
gnomAD - Exomes Ashkenazi Jewish Sub 10078 T=1.0000 G=0.0000
gnomAD - Exomes Other Sub 6128 T=1.000 G=0.000
TopMed Global Study-wide 125568 T=0.99564 G=0.00436
ExAC Global Study-wide 121268 T=0.99891 G=0.00109
ExAC Europe Sub 73326 T=1.0000 G=0.0000
ExAC Asian Sub 25146 T=1.0000 G=0.0000
ExAC American Sub 11482 T=0.9994 G=0.0006
ExAC African Sub 10406 T=0.9881 G=0.0119
ExAC Other Sub 908 T=1.00 G=0.00
The PAGE Study Global Study-wide 78702 T=0.9939 G=0.0061
The PAGE Study AfricanAmerican Sub 32516 T=0.9878 G=0.0122
The PAGE Study Mexican Sub 10810 T=0.9994 G=0.0006
The PAGE Study Asian Sub 8318 T=1.000 G=0.000
The PAGE Study PuertoRican Sub 7918 T=0.996 G=0.004
The PAGE Study NativeHawaiian Sub 4534 T=1.000 G=0.000
The PAGE Study Cuban Sub 4230 T=0.997 G=0.003
The PAGE Study Dominican Sub 3828 T=0.995 G=0.005
The PAGE Study CentralAmerican Sub 2450 T=0.998 G=0.002
The PAGE Study SouthAmerican Sub 1982 T=0.998 G=0.002
The PAGE Study NativeAmerican Sub 1260 T=0.997 G=0.003
The PAGE Study SouthAsian Sub 856 T=1.00 G=0.00
gnomAD - Genomes Global Study-wide 31400 T=0.9965 G=0.0035
gnomAD - Genomes European Sub 18904 T=1.0000 G=0.0000
gnomAD - Genomes African Sub 8710 T=0.988 G=0.012
gnomAD - Genomes East Asian Sub 1560 T=1.000 G=0.000
gnomAD - Genomes Other Sub 1088 T=0.999 G=0.001
gnomAD - Genomes American Sub 848 T=1.00 G=0.00
gnomAD - Genomes Ashkenazi Jewish Sub 290 T=1.00 G=0.00
GO Exome Sequencing Project Global Study-wide 12998 T=0.9961 G=0.0039
GO Exome Sequencing Project European American Sub 8592 T=1.000 G=0.000
GO Exome Sequencing Project African American Sub 4406 T=0.988 G=0.012
1000Genomes Global Study-wide 5008 T=0.997 G=0.003
1000Genomes African Sub 1322 T=0.988 G=0.012
1000Genomes East Asian Sub 1008 T=1.000 G=0.000
1000Genomes Europe Sub 1006 T=1.000 G=0.000
1000Genomes South Asian Sub 978 T=1.00 G=0.00
1000Genomes American Sub 694 T=1.00 G=0.00

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 T= G Note
GRCh38.p12 chr 3 NC_000003.12:g.120670449= NC_000003.12:g.12067044...


GRCh37.p13 chr 3 NC_000003.11:g.120389296= NC_000003.11:g.12038929...


HGD RefSeqGene NG_011957.1:g.17033= NG_011957.1:g.17033A>C
HGD transcript NM_000187.4:c.260= NM_000187.4:c.260A>C
HGD transcript NM_000187.3:c.260= NM_000187.3:c.260A>C
HGD transcript variant X5 XM_005247414.5:c.260= XM_005247414.5:c.260A>C
HGD transcript variant X3 XM_005247414.1:c.260= XM_005247414.1:c.260A>C
HGD transcript variant X3 XM_017006277.2:c.-164= XM_017006277.2:c.-164A>C
HGD transcript variant X1 XM_005247412.2:c.260= XM_005247412.2:c.260A>C
HGD transcript variant X1 XM_005247412.1:c.260= XM_005247412.1:c.260A>C
HGD transcript variant X2 XM_005247413.2:c.260= XM_005247413.2:c.260A>C
HGD transcript variant X2 XM_005247413.1:c.260= XM_005247413.1:c.260A>C
HGD transcript variant X4 XM_011512746.2:c.260= XM_011512746.2:c.260A>C
homogentisate 1,2-dioxygenase NP_000178.2:p.Glu87= NP_000178.2:p.Glu87Ala
homogentisate 1,2-dioxygenase isoform X5 XP_005247471.1:p.Glu87= XP_005247471.1:p.Glu87Ala
homogentisate 1,2-dioxygenase isoform X1 XP_005247469.1:p.Glu87= XP_005247469.1:p.Glu87Ala
homogentisate 1,2-dioxygenase isoform X2 XP_005247470.1:p.Glu87= XP_005247470.1:p.Glu87Ala
homogentisate 1,2-dioxygenase isoform X4 XP_011511048.1:p.Glu87= XP_011511048.1:p.Glu87Ala

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#.

36 SubSNP, 7 Frequency, 1 ClinVar submissions
No Submitter Submission ID Date (Build)
1 APPLERA_GI ss48419614 Mar 15, 2006 (126)
2 1000GENOMES ss331004975 May 09, 2011 (134)
3 NHLBI-ESP ss342144235 May 09, 2011 (134)
4 1000GENOMES ss489894720 May 04, 2012 (137)
5 EXOME_CHIP ss491344689 May 04, 2012 (137)
6 ILLUMINA ss534269752 Sep 08, 2015 (146)
7 ILLUMINA ss780820716 Sep 08, 2015 (146)
8 ILLUMINA ss783503133 Sep 08, 2015 (146)
9 1000GENOMES ss1305860183 Aug 21, 2014 (142)
10 EVA_EXAC ss1687158521 Apr 01, 2015 (144)
11 ILLUMINA ss1752435081 Sep 08, 2015 (146)
12 ILLUMINA ss1917771372 Feb 12, 2016 (147)
13 WEILL_CORNELL_DGM ss1922310269 Feb 12, 2016 (147)
14 ILLUMINA ss1946093453 Feb 12, 2016 (147)
15 ILLUMINA ss1958598419 Feb 12, 2016 (147)
16 HUMAN_LONGEVITY ss2255254800 Dec 20, 2016 (150)
17 TOPMED ss2422579232 Dec 20, 2016 (150)
18 GNOMAD ss2733990632 Nov 08, 2017 (151)
19 GNOMAD ss2747077635 Nov 08, 2017 (151)
20 GNOMAD ss2798281793 Nov 08, 2017 (151)
21 AFFY ss2985267492 Nov 08, 2017 (151)
22 ILLUMINA ss3022278791 Nov 08, 2017 (151)
23 TOPMED ss3403602859 Nov 08, 2017 (151)
24 ILLUMINA ss3628759189 Oct 12, 2018 (152)
25 ILLUMINA ss3628759190 Oct 12, 2018 (152)
26 ILLUMINA ss3634913380 Oct 12, 2018 (152)
27 ILLUMINA ss3640620679 Oct 12, 2018 (152)
28 ILLUMINA ss3644826083 Oct 12, 2018 (152)
29 ILLUMINA ss3652757315 Oct 12, 2018 (152)
30 ILLUMINA ss3654036565 Oct 12, 2018 (152)
31 ILLUMINA ss3726050109 Jul 13, 2019 (153)
32 ILLUMINA ss3744514709 Jul 13, 2019 (153)
33 ILLUMINA ss3745213342 Jul 13, 2019 (153)
34 PAGE_CC ss3771058437 Jul 13, 2019 (153)
35 ILLUMINA ss3772708648 Jul 13, 2019 (153)
36 KHV_HUMAN_GENOMES ss3803735806 Jul 13, 2019 (153)
37 1000Genomes NC_000003.11 - 120389296 Oct 12, 2018 (152)
38 ExAC NC_000003.11 - 120389296 Oct 12, 2018 (152)
39 gnomAD - Genomes NC_000003.11 - 120389296 Jul 13, 2019 (153)
40 gnomAD - Exomes NC_000003.11 - 120389296 Jul 13, 2019 (153)
41 GO Exome Sequencing Project NC_000003.11 - 120389296 Oct 12, 2018 (152)
42 The PAGE Study NC_000003.12 - 120670449 Jul 13, 2019 (153)
43 TopMed NC_000003.12 - 120670449 Oct 12, 2018 (152)
44 ClinVar RCV000400316.1 Oct 12, 2018 (152)

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
17112878, 7094453, 46817343, 3076130, 403769, ss331004975, ss342144235, ss489894720, ss491344689, ss534269752, ss780820716, ss783503133, ss1305860183, ss1687158521, ss1752435081, ss1917771372, ss1922310269, ss1946093453, ss1958598419, ss2422579232, ss2733990632, ss2747077635, ss2798281793, ss2985267492, ss3022278791, ss3628759189, ss3628759190, ss3634913380, ss3640620679, ss3644826083, ss3652757315, ss3654036565, ss3744514709, ss3745213342, ss3772708648 NC_000003.11:120389295:T:G NC_000003.12:120670448:T:G (self)
RCV000400316.1, 279906, 261524235, ss2255254800, ss3403602859, ss3726050109, ss3771058437, ss3803735806 NC_000003.12:120670448:T:G NC_000003.12:120670448:T:G (self)
ss48419614 NT_005612.16:26884441:T:G NC_000003.12:120670448:T:G (self)

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

1 citation for rs35702995
PMID Title Author Year Journal
22606059 Computational methods to work as first-pass filter in deleterious SNP analysis of alkaptonuria. Magesh R et al. 2012 TheScientificWorldJournal

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.post246+3cda961