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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.

rs2255543

Current Build 153

Released July 9, 2019

Organism
Homo sapiens
Position
chr3:120670469 (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
T>A
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.25934 (65173/251302, GnomAD_exome)
T=0.24982 (31370/125568, TOPMED)
T=0.26467 (32106/121306, ExAC) (+ 8 more)
T=0.2440 (19195/78684, PAGE_STUDY)
T=0.2605 (8158/31314, GnomAD)
T=0.2566 (3335/12998, GO-ESP)
T=0.268 (1344/5008, 1000G)
T=0.287 (1287/4480, Estonian)
T=0.269 (1038/3854, ALSPAC)
T=0.266 (986/3708, TWINSUK)
T=0.27 (160/600, NorthernSweden)
Clinical Significance
Reported in ClinVar
Gene : Consequence
HGD : Missense Variant
Publications
3 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.120670469T>A
GRCh37.p13 chr 3 NC_000003.11:g.120389316T>A
HGD RefSeqGene NG_011957.1:g.17013A>T
Gene: HGD, homogentisate 1,2-dioxygenase (minus strand)
Molecule type Change Amino acid[Codon] SO Term
HGD transcript NM_000187.4:c.240A>T Q [CAA] > H [CAT] Coding Sequence Variant
homogentisate 1,2-dioxygenase NP_000178.2:p.Gln80His Q (Gln) > H (His) Missense Variant
HGD transcript variant X3 XM_017006277.2:c. N/A 5 Prime UTR Variant
HGD transcript variant X1 XM_005247412.2:c.240A>T Q [CAA] > H [CAT] Coding Sequence Variant
homogentisate 1,2-dioxygenase isoform X1 XP_005247469.1:p.Gln80His Q (Gln) > H (His) Missense Variant
HGD transcript variant X2 XM_005247413.2:c.240A>T Q [CAA] > H [CAT] Coding Sequence Variant
homogentisate 1,2-dioxygenase isoform X2 XP_005247470.1:p.Gln80His Q (Gln) > H (His) Missense Variant
HGD transcript variant X4 XM_011512746.2:c.240A>T Q [CAA] > H [CAT] Coding Sequence Variant
homogentisate 1,2-dioxygenase isoform X4 XP_011511048.1:p.Gln80His Q (Gln) > H (His) Missense Variant
HGD transcript variant X5 XM_005247414.5:c.240A>T Q [CAA] > H [CAT] Coding Sequence Variant
homogentisate 1,2-dioxygenase isoform X5 XP_005247471.1:p.Gln80His Q (Gln) > H (His) Missense 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: 250852 )
ClinVar Accession Disease Names Clinical Significance
RCV000252512.1 not specified Benign
RCV000306096.1 Alkaptonuria Benign
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 251302 T=0.25934 A=0.74066
gnomAD - Exomes European Sub 135310 T=0.26163 A=0.73837
gnomAD - Exomes Asian Sub 49008 T=0.3199 A=0.6801
gnomAD - Exomes American Sub 34534 T=0.1860 A=0.8140
gnomAD - Exomes African Sub 16250 T=0.2385 A=0.7615
gnomAD - Exomes Ashkenazi Jewish Sub 10076 T=0.2256 A=0.7744
gnomAD - Exomes Other Sub 6124 T=0.248 A=0.752
TopMed Global Study-wide 125568 T=0.24982 A=0.75018
ExAC Global Study-wide 121306 T=0.26467 A=0.73533
ExAC Europe Sub 73336 T=0.2614 A=0.7386
ExAC Asian Sub 25144 T=0.3183 A=0.6817
ExAC American Sub 11514 T=0.1930 A=0.8070
ExAC African Sub 10404 T=0.2372 A=0.7628
ExAC Other Sub 908 T=0.27 A=0.73
The PAGE Study Global Study-wide 78684 T=0.2440 A=0.7560
The PAGE Study AfricanAmerican Sub 32512 T=0.2435 A=0.7565
The PAGE Study Mexican Sub 10806 T=0.1874 A=0.8126
The PAGE Study Asian Sub 8314 T=0.424 A=0.576
The PAGE Study PuertoRican Sub 7916 T=0.199 A=0.801
The PAGE Study NativeHawaiian Sub 4532 T=0.192 A=0.808
The PAGE Study Cuban Sub 4230 T=0.225 A=0.775
The PAGE Study Dominican Sub 3828 T=0.230 A=0.770
The PAGE Study CentralAmerican Sub 2450 T=0.205 A=0.795
The PAGE Study SouthAmerican Sub 1982 T=0.199 A=0.801
The PAGE Study NativeAmerican Sub 1260 T=0.229 A=0.771
The PAGE Study SouthAsian Sub 854 T=0.30 A=0.70
gnomAD - Genomes Global Study-wide 31314 T=0.2605 A=0.7395
gnomAD - Genomes European Sub 18864 T=0.2669 A=0.7331
gnomAD - Genomes African Sub 8684 T=0.239 A=0.761
gnomAD - Genomes East Asian Sub 1548 T=0.354 A=0.646
gnomAD - Genomes Other Sub 1086 T=0.269 A=0.731
gnomAD - Genomes American Sub 844 T=0.18 A=0.82
gnomAD - Genomes Ashkenazi Jewish Sub 288 T=0.19 A=0.81
GO Exome Sequencing Project Global Study-wide 12998 T=0.2566 A=0.7434
GO Exome Sequencing Project European American Sub 8592 T=0.264 A=0.736
GO Exome Sequencing Project African American Sub 4406 T=0.243 A=0.757
1000Genomes Global Study-wide 5008 T=0.268 A=0.732
1000Genomes African Sub 1322 T=0.218 A=0.782
1000Genomes East Asian Sub 1008 T=0.357 A=0.643
1000Genomes Europe Sub 1006 T=0.235 A=0.765
1000Genomes South Asian Sub 978 T=0.34 A=0.66
1000Genomes American Sub 694 T=0.19 A=0.81
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.287 A=0.713
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.269 A=0.731
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.266 A=0.734
Northern Sweden ACPOP Study-wide 600 T=0.27 A=0.73
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 T= A Note
GRCh38.p12 chr 3 NC_000003.12:g.120670469= NC_000003.12:g.12067046...

NC_000003.12:g.120670469T>A

GRCh37.p13 chr 3 NC_000003.11:g.120389316= NC_000003.11:g.12038931...

NC_000003.11:g.120389316T>A

HGD RefSeqGene NG_011957.1:g.17013= NG_011957.1:g.17013A>T
HGD transcript NM_000187.4:c.240= NM_000187.4:c.240A>T
HGD transcript NM_000187.3:c.240= NM_000187.3:c.240A>T
HGD transcript variant X5 XM_005247414.5:c.240= XM_005247414.5:c.240A>T
HGD transcript variant X3 XM_005247414.1:c.240= XM_005247414.1:c.240A>T
HGD transcript variant X3 XM_017006277.2:c.-184= XM_017006277.2:c.-184A>T
HGD transcript variant X1 XM_005247412.2:c.240= XM_005247412.2:c.240A>T
HGD transcript variant X1 XM_005247412.1:c.240= XM_005247412.1:c.240A>T
HGD transcript variant X2 XM_005247413.2:c.240= XM_005247413.2:c.240A>T
HGD transcript variant X2 XM_005247413.1:c.240= XM_005247413.1:c.240A>T
HGD transcript variant X4 XM_011512746.2:c.240= XM_011512746.2:c.240A>T
homogentisate 1,2-dioxygenase NP_000178.2:p.Gln80= NP_000178.2:p.Gln80His
homogentisate 1,2-dioxygenase isoform X5 XP_005247471.1:p.Gln80= XP_005247471.1:p.Gln80His
homogentisate 1,2-dioxygenase isoform X1 XP_005247469.1:p.Gln80= XP_005247469.1:p.Gln80His
homogentisate 1,2-dioxygenase isoform X2 XP_005247470.1:p.Gln80= XP_005247470.1:p.Gln80His
homogentisate 1,2-dioxygenase isoform X4 XP_011511048.1:p.Gln80= XP_011511048.1:p.Gln80His
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#.

96 SubSNP, 11 Frequency, 2 ClinVar submissions
No Submitter Submission ID Date (Build)
1 YUSUKE ss3207701 Sep 28, 2001 (100)
2 SC_JCM ss3859235 Sep 28, 2001 (100)
3 PERLEGEN ss23899003 Sep 20, 2004 (123)
4 MGC_GENOME_DIFF ss28510919 Sep 24, 2004 (126)
5 APPLERA_GI ss48430079 Mar 11, 2006 (126)
6 PERLEGEN ss68873518 May 17, 2007 (127)
7 BCMHGSC_JDW ss92257424 Mar 23, 2008 (130)
8 HUMANGENOME_JCVI ss99127282 Feb 06, 2009 (130)
9 BGI ss103978163 Dec 01, 2009 (131)
10 ENSEMBL ss139451520 Dec 01, 2009 (131)
11 ENSEMBL ss139685872 Dec 01, 2009 (131)
12 GMI ss156111504 Dec 01, 2009 (131)
13 ILLUMINA ss161076509 Dec 01, 2009 (131)
14 COMPLETE_GENOMICS ss162547836 Jul 04, 2010 (132)
15 COMPLETE_GENOMICS ss164110917 Jul 04, 2010 (132)
16 COMPLETE_GENOMICS ss167113112 Jul 04, 2010 (132)
17 ILLUMINA ss169027894 Jul 04, 2010 (132)
18 BUSHMAN ss203091556 Jul 04, 2010 (132)
19 BCM-HGSC-SUB ss206148084 Jul 04, 2010 (132)
20 BL ss253439388 May 09, 2011 (134)
21 GMI ss277320427 May 04, 2012 (137)
22 GMI ss284734958 Apr 25, 2013 (138)
23 1000GENOMES ss331004976 May 09, 2011 (134)
24 NHLBI-ESP ss342144236 May 09, 2011 (134)
25 ILLUMINA ss479457906 Sep 08, 2015 (146)
26 ILLUMINA ss484251532 May 04, 2012 (137)
27 ILLUMINA ss484445018 May 04, 2012 (137)
28 1000GENOMES ss489894722 May 04, 2012 (137)
29 EXOME_CHIP ss491344690 May 04, 2012 (137)
30 ILLUMINA ss536437218 Sep 08, 2015 (146)
31 TISHKOFF ss556900242 Apr 25, 2013 (138)
32 SSMP ss650612127 Apr 25, 2013 (138)
33 ILLUMINA ss779529758 Sep 08, 2015 (146)
34 ILLUMINA ss780820717 Sep 08, 2015 (146)
35 ILLUMINA ss782571812 Sep 08, 2015 (146)
36 ILLUMINA ss783503134 Sep 08, 2015 (146)
37 ILLUMINA ss835000309 Sep 08, 2015 (146)
38 JMKIDD_LAB ss974449391 Aug 21, 2014 (142)
39 EVA-GONL ss979083941 Aug 21, 2014 (142)
40 JMKIDD_LAB ss1067454151 Aug 21, 2014 (142)
41 JMKIDD_LAB ss1070777392 Aug 21, 2014 (142)
42 1000GENOMES ss1305860184 Aug 21, 2014 (142)
43 DDI ss1429564118 Apr 01, 2015 (144)
44 EVA_GENOME_DK ss1580152579 Apr 01, 2015 (144)
45 EVA_FINRISK ss1584029646 Apr 01, 2015 (144)
46 EVA_DECODE ss1588566160 Apr 01, 2015 (144)
47 EVA_UK10K_ALSPAC ss1608059710 Apr 01, 2015 (144)
48 EVA_UK10K_TWINSUK ss1651053743 Apr 01, 2015 (144)
49 EVA_EXAC ss1687158524 Apr 01, 2015 (144)
50 EVA_MGP ss1711029906 Apr 01, 2015 (144)
51 ILLUMINA ss1752435082 Sep 08, 2015 (146)
52 HAMMER_LAB ss1799930864 Sep 08, 2015 (146)
53 ILLUMINA ss1917771373 Feb 12, 2016 (147)
54 WEILL_CORNELL_DGM ss1922310270 Feb 12, 2016 (147)
55 ILLUMINA ss1946093454 Feb 12, 2016 (147)
56 ILLUMINA ss1958598420 Feb 12, 2016 (147)
57 GENOMED ss1969505823 Jul 19, 2016 (147)
58 JJLAB ss2021722972 Sep 14, 2016 (149)
59 USC_VALOUEV ss2149815106 Dec 20, 2016 (150)
60 HUMAN_LONGEVITY ss2255254802 Dec 20, 2016 (150)
61 TOPMED ss2422579233 Dec 20, 2016 (150)
62 SYSTEMSBIOZJU ss2625363326 Nov 08, 2017 (151)
63 ILLUMINA ss2634003257 Nov 08, 2017 (151)
64 GRF ss2705218406 Nov 08, 2017 (151)
65 GNOMAD ss2733990638 Nov 08, 2017 (151)
66 GNOMAD ss2747077637 Nov 08, 2017 (151)
67 GNOMAD ss2798281795 Nov 08, 2017 (151)
68 AFFY ss2985267493 Nov 08, 2017 (151)
69 SWEGEN ss2993074627 Nov 08, 2017 (151)
70 EVA_SAMSUNG_MC ss3023059788 Nov 08, 2017 (151)
71 BIOINF_KMB_FNS_UNIBA ss3024628319 Nov 08, 2017 (151)
72 CSHL ss3345231489 Nov 08, 2017 (151)
73 TOPMED ss3403602862 Nov 08, 2017 (151)
74 ILLUMINA ss3628759191 Oct 12, 2018 (152)
75 ILLUMINA ss3628759192 Oct 12, 2018 (152)
76 ILLUMINA ss3631946585 Oct 12, 2018 (152)
77 ILLUMINA ss3634913381 Oct 12, 2018 (152)
78 ILLUMINA ss3636609772 Oct 12, 2018 (152)
79 ILLUMINA ss3638437545 Oct 12, 2018 (152)
80 ILLUMINA ss3640620680 Oct 12, 2018 (152)
81 ILLUMINA ss3644826084 Oct 12, 2018 (152)
82 OMUKHERJEE_ADBS ss3646291550 Oct 12, 2018 (152)
83 URBANLAB ss3647510534 Oct 12, 2018 (152)
84 ILLUMINA ss3654036566 Oct 12, 2018 (152)
85 EGCUT_WGS ss3661001390 Jul 13, 2019 (153)
86 EVA_DECODE ss3710145730 Jul 13, 2019 (153)
87 ACPOP ss3730286856 Jul 13, 2019 (153)
88 ILLUMINA ss3744514710 Jul 13, 2019 (153)
89 ILLUMINA ss3745213343 Jul 13, 2019 (153)
90 EVA ss3760599526 Jul 13, 2019 (153)
91 PAGE_CC ss3771058438 Jul 13, 2019 (153)
92 ILLUMINA ss3772708649 Jul 13, 2019 (153)
93 PACBIO ss3784443335 Jul 13, 2019 (153)
94 PACBIO ss3789940783 Jul 13, 2019 (153)
95 PACBIO ss3794815218 Jul 13, 2019 (153)
96 KHV_HUMAN_GENOMES ss3803735807 Jul 13, 2019 (153)
97 1000Genomes NC_000003.11 - 120389316 Oct 12, 2018 (152)
98 The Avon Longitudinal Study of Parents and Children NC_000003.11 - 120389316 Oct 12, 2018 (152)
99 Genetic variation in the Estonian population NC_000003.11 - 120389316 Oct 12, 2018 (152)
100 ExAC NC_000003.11 - 120389316 Oct 12, 2018 (152)
101 gnomAD - Genomes NC_000003.11 - 120389316 Jul 13, 2019 (153)
102 gnomAD - Exomes NC_000003.11 - 120389316 Jul 13, 2019 (153)
103 GO Exome Sequencing Project NC_000003.11 - 120389316 Oct 12, 2018 (152)
104 Northern Sweden NC_000003.11 - 120389316 Jul 13, 2019 (153)
105 The PAGE Study NC_000003.12 - 120670469 Jul 13, 2019 (153)
106 TopMed NC_000003.12 - 120670469 Oct 12, 2018 (152)
107 UK 10K study - Twins NC_000003.11 - 120389316 Oct 12, 2018 (152)
108 ClinVar RCV000252512.1 Oct 12, 2018 (152)
109 ClinVar RCV000306096.1 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).

Associated ID History Updated (Build)
rs17140273 Oct 07, 2004 (123)
rs17856617 Mar 11, 2006 (126)
rs61795578 May 25, 2008 (130)
rs386505110 Aug 21, 2014 (142)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss92257424, ss162547836, ss164110917, ss167113112, ss203091556, ss206148084, ss253439388, ss277320427, ss284734958, ss484445018, ss1588566160 NC_000003.10:121872005:T:A NC_000003.12:120670468:T:A (self)
17112879, 9532634, 6739638, 7094456, 46817345, 3076136, 403771, 3571721, 9532634, ss331004976, ss342144236, ss479457906, ss484251532, ss489894722, ss491344690, ss536437218, ss556900242, ss650612127, ss779529758, ss780820717, ss782571812, ss783503134, ss835000309, ss974449391, ss979083941, ss1067454151, ss1070777392, ss1305860184, ss1429564118, ss1580152579, ss1584029646, ss1608059710, ss1651053743, ss1687158524, ss1711029906, ss1752435082, ss1799930864, ss1917771373, ss1922310270, ss1946093454, ss1958598420, ss1969505823, ss2021722972, ss2149815106, ss2422579233, ss2625363326, ss2634003257, ss2705218406, ss2733990638, ss2747077637, ss2798281795, ss2985267493, ss2993074627, ss3023059788, ss3345231489, ss3628759191, ss3628759192, ss3631946585, ss3634913381, ss3636609772, ss3638437545, ss3640620680, ss3644826084, ss3646291550, ss3654036566, ss3661001390, ss3730286856, ss3744514710, ss3745213343, ss3760599526, ss3772708649, ss3784443335, ss3789940783, ss3794815218 NC_000003.11:120389315:T:A NC_000003.12:120670468:T:A (self)
RCV000252512.1, RCV000306096.1, 279907, 261524238, ss2255254802, ss3024628319, ss3403602862, ss3647510534, ss3710145730, ss3771058438, ss3803735807 NC_000003.12:120670468:T:A NC_000003.12:120670468:T:A (self)
ss3207701, ss3859235, ss23899003, ss28510919, ss48430079, ss68873518, ss99127282, ss103978163, ss139451520, ss139685872, ss156111504, ss161076509, ss169027894 NT_005612.16:26884461:T:A NC_000003.12:120670468:T:A (self)
Help

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

3 citations for rs2255543
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
25741868 Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Richards S et al. 2015 Genetics in medicine
26960557 A Founder Effect for the HGD G360R Mutation in Italy: Implications for a Regional Screening of Alkaptonuria. Porfirio B et al. 2016 JIMD reports

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