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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
chr3:120670449 (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
G=0.004454 (1179/264690, TOPMED)
G=0.000836 (210/251280, GnomAD_exome)
G=0.000421 (84/199668, ALFA) (+ 8 more)
G=0.004164 (584/140238, GnomAD)
G=0.001088 (132/121268, ExAC)
G=0.00606 (477/78702, PAGE_STUDY)
G=0.00392 (51/12998, GO-ESP)
G=0.0032 (16/5008, 1000G)
G=0.009 (2/216, Qatari)
T=0.5 (1/2, SGDP_PRJ)
G=0.5 (1/2, SGDP_PRJ)
Clinical Significance
Reported in ClinVar
Gene : Consequence
HGD : Missense Variant
1 citation
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 199668 T=0.999579 G=0.000421
European Sub 170004 T=0.999982 G=0.000018
African Sub 4992 T=0.9854 G=0.0146
African Others Sub 176 T=0.949 G=0.051
African American Sub 4816 T=0.9867 G=0.0133
Asian Sub 6354 T=1.0000 G=0.0000
East Asian Sub 4504 T=1.0000 G=0.0000
Other Asian Sub 1850 T=1.0000 G=0.0000
Latin American 1 Sub 804 T=0.998 G=0.002
Latin American 2 Sub 974 T=0.999 G=0.001
South Asian Sub 280 T=1.000 G=0.000
Other Sub 16260 T=0.99969 G=0.00031


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 T=0.995546 G=0.004454
gnomAD - Exomes Global Study-wide 251280 T=0.999164 G=0.000836
gnomAD - Exomes European Sub 135290 T=1.000000 G=0.000000
gnomAD - Exomes Asian Sub 48998 T=0.99994 G=0.00006
gnomAD - Exomes American Sub 34534 T=0.99962 G=0.00038
gnomAD - Exomes African Sub 16252 T=0.98819 G=0.01181
gnomAD - Exomes Ashkenazi Jewish Sub 10078 T=1.00000 G=0.00000
gnomAD - Exomes Other Sub 6128 T=0.9997 G=0.0003
gnomAD - Genomes Global Study-wide 140238 T=0.995836 G=0.004164
gnomAD - Genomes European Sub 75950 T=0.99995 G=0.00005
gnomAD - Genomes African Sub 42036 T=0.98684 G=0.01316
gnomAD - Genomes American Sub 13640 T=0.99853 G=0.00147
gnomAD - Genomes Ashkenazi Jewish Sub 3324 T=1.0000 G=0.0000
gnomAD - Genomes East Asian Sub 3134 T=1.0000 G=0.0000
gnomAD - Genomes Other Sub 2154 T=0.9968 G=0.0032
ExAC Global Study-wide 121268 T=0.998912 G=0.001088
ExAC Europe Sub 73326 T=1.00000 G=0.00000
ExAC Asian Sub 25146 T=0.99996 G=0.00004
ExAC American Sub 11482 T=0.99939 G=0.00061
ExAC African Sub 10406 T=0.98808 G=0.01192
ExAC Other Sub 908 T=1.000 G=0.000
The PAGE Study Global Study-wide 78702 T=0.99394 G=0.00606
The PAGE Study AfricanAmerican Sub 32516 T=0.98776 G=0.01224
The PAGE Study Mexican Sub 10810 T=0.99944 G=0.00056
The PAGE Study Asian Sub 8318 T=1.0000 G=0.0000
The PAGE Study PuertoRican Sub 7918 T=0.9962 G=0.0038
The PAGE Study NativeHawaiian Sub 4534 T=1.0000 G=0.0000
The PAGE Study Cuban Sub 4230 T=0.9972 G=0.0028
The PAGE Study Dominican Sub 3828 T=0.9950 G=0.0050
The PAGE Study CentralAmerican Sub 2450 T=0.9980 G=0.0020
The PAGE Study SouthAmerican Sub 1982 T=0.9985 G=0.0015
The PAGE Study NativeAmerican Sub 1260 T=0.9968 G=0.0032
The PAGE Study SouthAsian Sub 856 T=1.000 G=0.000
GO Exome Sequencing Project Global Study-wide 12998 T=0.99608 G=0.00392
GO Exome Sequencing Project European American Sub 8592 T=1.0000 G=0.0000
GO Exome Sequencing Project African American Sub 4406 T=0.9884 G=0.0116
1000Genomes Global Study-wide 5008 T=0.9968 G=0.0032
1000Genomes African Sub 1322 T=0.9879 G=0.0121
1000Genomes East Asian Sub 1008 T=1.0000 G=0.0000
1000Genomes Europe Sub 1006 T=1.0000 G=0.0000
1000Genomes South Asian Sub 978 T=1.000 G=0.000
1000Genomes American Sub 694 T=1.000 G=0.000
Qatari Global Study-wide 216 T=0.991 G=0.009
SGDP_PRJ Global Study-wide 2 T=0.5 G=0.5

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.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.-164= 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 X6 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
RCV000400316.3 Alkaptonuria Benign

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
GRCh38.p13 chr 3 NC_000003.12:g.120670449= NC_000003.12:g.120670449T>G
GRCh37.p13 chr 3 NC_000003.11:g.120389296= NC_000003.11:g.120389296T>G
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 X6 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#.

40 SubSNP, 10 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 EVA ss3823945464 Apr 25, 2020 (154)
38 SGDP_PRJ ss3856814239 Apr 25, 2020 (154)
39 EVA ss3986250782 Apr 26, 2021 (155)
40 TOPMED ss4581097561 Apr 26, 2021 (155)
41 1000Genomes NC_000003.11 - 120389296 Oct 12, 2018 (152)
42 ExAC NC_000003.11 - 120389296 Oct 12, 2018 (152)
43 gnomAD - Genomes NC_000003.12 - 120670449 Apr 26, 2021 (155)
44 gnomAD - Exomes NC_000003.11 - 120389296 Jul 13, 2019 (153)
45 GO Exome Sequencing Project NC_000003.11 - 120389296 Oct 12, 2018 (152)
46 The PAGE Study NC_000003.12 - 120670449 Jul 13, 2019 (153)
47 Qatari NC_000003.11 - 120389296 Apr 25, 2020 (154)
48 SGDP_PRJ NC_000003.11 - 120389296 Apr 25, 2020 (154)
49 TopMed NC_000003.12 - 120670449 Apr 26, 2021 (155)
50 ALFA NC_000003.12 - 120670449 Apr 26, 2021 (155)
51 ClinVar RCV000400316.3 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
17112878, 7094453, 3076130, 403769, 4352199, 8831219, 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, ss3823945464, ss3856814239, ss3986250782 NC_000003.11:120389295:T:G NC_000003.12:120670448:T:G (self)
RCV000400316.3, 121670656, 279906, 261524235, 418475116, 2354978168, ss2255254800, ss3403602859, ss3726050109, ss3771058437, ss3803735806, ss4581097561 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

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