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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.

rs120074173

Current Build 153

Released July 9, 2019

Organism
Homo sapiens
Position
chr3:120633233 (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>C
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.00017 (42/251288, GnomAD_exome)
C=0.00031 (39/125568, TOPMED)
C=0.00013 (16/121354, ExAC) (+ 6 more)
C=0.0001 (8/78686, PAGE_STUDY)
C=0.0003 (9/31374, GnomAD)
C=0.001 (3/5008, 1000G)
C=0.001 (3/4480, Estonian)
C=0.000 (1/3854, ALSPAC)
C=0.000 (0/3708, TWINSUK)
Clinical Significance
Reported in ClinVar
Gene : Consequence
HGD : Missense Variant
Publications
4 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.120633233T>C
GRCh37.p13 chr 3 NC_000003.11:g.120352080T>C
HGD RefSeqGene NG_011957.1:g.54249A>G
Gene: HGD, homogentisate 1,2-dioxygenase (minus strand)
Molecule type Change Amino acid[Codon] SO Term
HGD transcript NM_000187.4:c.1102A>G M [ATG] > V [GTG] Coding Sequence Variant
homogentisate 1,2-dioxygenase NP_000178.2:p.Met368Val M (Met) > V (Val) Missense Variant
HGD transcript variant X2 XM_005247413.2:c. N/A Genic Downstream Transcript Variant
HGD transcript variant X5 XM_005247414.5:c. N/A Genic Downstream Transcript Variant
HGD transcript variant X4 XM_011512746.2:c. N/A Genic Downstream Transcript Variant
HGD transcript variant X1 XM_005247412.2:c.877A>G M [ATG] > V [GTG] Coding Sequence Variant
homogentisate 1,2-dioxygenase isoform X1 XP_005247469.1:p.Met293Val M (Met) > V (Val) Missense Variant
HGD transcript variant X3 XM_017006277.2:c.679A>G M [ATG] > V [GTG] Coding Sequence Variant
homogentisate 1,2-dioxygenase isoform X3 XP_016861766.1:p.Met227Val M (Met) > V (Val) 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: C (allele ID: 18212 )
ClinVar Accession Disease Names Clinical Significance
RCV000003323.9 Alkaptonuria Pathogenic
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").

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Study Population Group Sample Size Ref Allele Alt Allele
gnomAD - Exomes Global Study-wide 251288 T=0.99983 C=0.00017
gnomAD - Exomes European Sub 135234 T=0.99971 C=0.00029
gnomAD - Exomes Asian Sub 49006 T=1.0000 C=0.0000
gnomAD - Exomes American Sub 34588 T=1.0000 C=0.0000
gnomAD - Exomes African Sub 16256 T=0.9999 C=0.0001
gnomAD - Exomes Ashkenazi Jewish Sub 10076 T=1.0000 C=0.0000
gnomAD - Exomes Other Sub 6128 T=1.000 C=0.000
TopMed Global Study-wide 125568 T=0.99969 C=0.00031
ExAC Global Study-wide 121354 T=0.99987 C=0.00013
ExAC Europe Sub 73316 T=0.9998 C=0.0002
ExAC Asian Sub 25152 T=1.0000 C=0.0000
ExAC American Sub 11576 T=1.0000 C=0.0000
ExAC African Sub 10402 T=1.0000 C=0.0000
ExAC Other Sub 908 T=1.00 C=0.00
The PAGE Study Global Study-wide 78686 T=0.9999 C=0.0001
The PAGE Study AfricanAmerican Sub 32512 T=0.9998 C=0.0002
The PAGE Study Mexican Sub 10808 T=1.0000 C=0.0000
The PAGE Study Asian Sub 8316 T=1.000 C=0.000
The PAGE Study PuertoRican Sub 7918 T=1.000 C=0.000
The PAGE Study NativeHawaiian Sub 4530 T=1.000 C=0.000
The PAGE Study Cuban Sub 4230 T=1.000 C=0.000
The PAGE Study Dominican Sub 3826 T=1.000 C=0.000
The PAGE Study CentralAmerican Sub 2450 T=1.000 C=0.000
The PAGE Study SouthAmerican Sub 1980 T=1.000 C=0.000
The PAGE Study NativeAmerican Sub 1260 T=1.000 C=0.000
The PAGE Study SouthAsian Sub 856 T=1.00 C=0.00
gnomAD - Genomes Global Study-wide 31374 T=0.9997 C=0.0003
gnomAD - Genomes European Sub 18894 T=0.9995 C=0.0005
gnomAD - Genomes African Sub 8698 T=1.000 C=0.000
gnomAD - Genomes East Asian Sub 1560 T=1.000 C=0.000
gnomAD - Genomes Other Sub 1084 T=1.000 C=0.000
gnomAD - Genomes American Sub 848 T=1.00 C=0.00
gnomAD - Genomes Ashkenazi Jewish Sub 290 T=1.00 C=0.00
1000Genomes Global Study-wide 5008 T=0.999 C=0.001
1000Genomes African Sub 1322 T=1.000 C=0.000
1000Genomes East Asian Sub 1008 T=1.000 C=0.000
1000Genomes Europe Sub 1006 T=0.997 C=0.003
1000Genomes South Asian Sub 978 T=1.00 C=0.00
1000Genomes American Sub 694 T=1.00 C=0.00
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.999 C=0.001
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=1.000 C=0.000
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=1.000 C=0.000
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= C Note
GRCh38.p12 chr 3 NC_000003.12:g.120633233= NC_000003.12:g.12063323...

NC_000003.12:g.120633233T>C

GRCh37.p13 chr 3 NC_000003.11:g.120352080= NC_000003.11:g.12035208...

NC_000003.11:g.120352080T>C

HGD RefSeqGene NG_011957.1:g.54249= NG_011957.1:g.54249A>G
HGD transcript NM_000187.4:c.1102= NM_000187.4:c.1102A>G
HGD transcript NM_000187.3:c.1102= NM_000187.3:c.1102A>G
HGD transcript variant X3 XM_017006277.2:c.679= XM_017006277.2:c.679A>G
HGD transcript variant X1 XM_005247412.2:c.877= XM_005247412.2:c.877A>G
HGD transcript variant X1 XM_005247412.1:c.877= XM_005247412.1:c.877A>G
homogentisate 1,2-dioxygenase NP_000178.2:p.Met368= NP_000178.2:p.Met368Val
homogentisate 1,2-dioxygenase isoform X3 XP_016861766.1:p.Met227= XP_016861766.1:p.Met227Val
homogentisate 1,2-dioxygenase isoform X1 XP_005247469.1:p.Met293= XP_005247469.1:p.Met293Val
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#.

30 SubSNP, 9 Frequency, 1 ClinVar submissions
No Submitter Submission ID Date (Build)
1 OMIM-CURATED-RECORDS ss255605807 Aug 20, 2010 (132)
2 NHLBI-ESP ss342144220 May 09, 2011 (134)
3 1000GENOMES ss488765863 May 04, 2012 (137)
4 EXOME_CHIP ss491344684 May 04, 2012 (137)
5 ILLUMINA ss780820711 Sep 08, 2015 (146)
6 ILLUMINA ss783503128 Sep 08, 2015 (146)
7 1000GENOMES ss1305859138 Aug 21, 2014 (142)
8 EVA_UK10K_ALSPAC ss1608059109 Apr 01, 2015 (144)
9 EVA_UK10K_TWINSUK ss1651053142 Apr 01, 2015 (144)
10 EVA_EXAC ss1687158206 Apr 01, 2015 (144)
11 ILLUMINA ss1917771367 Feb 12, 2016 (147)
12 ILLUMINA ss1946093441 Feb 12, 2016 (147)
13 ILLUMINA ss1958598388 Feb 12, 2016 (147)
14 JJLAB ss2021722790 Sep 14, 2016 (149)
15 HUMAN_LONGEVITY ss2255252641 Dec 20, 2016 (150)
16 TOPMED ss2422577097 Dec 20, 2016 (150)
17 GNOMAD ss2733990156 Nov 08, 2017 (151)
18 GNOMAD ss2747077504 Nov 08, 2017 (151)
19 GNOMAD ss2798279091 Nov 08, 2017 (151)
20 AFFY ss2985267472 Nov 08, 2017 (151)
21 TOPMED ss3403596423 Nov 08, 2017 (151)
22 ILLUMINA ss3628759117 Oct 12, 2018 (152)
23 ILLUMINA ss3634913375 Oct 12, 2018 (152)
24 ILLUMINA ss3640620674 Oct 12, 2018 (152)
25 ILLUMINA ss3644826072 Oct 12, 2018 (152)
26 ILLUMINA ss3654036544 Oct 12, 2018 (152)
27 EGCUT_WGS ss3661000928 Jul 13, 2019 (153)
28 ILLUMINA ss3744514704 Jul 13, 2019 (153)
29 ILLUMINA ss3745213337 Jul 13, 2019 (153)
30 PAGE_CC ss3771058409 Jul 13, 2019 (153)
31 1000Genomes NC_000003.11 - 120352080 Oct 12, 2018 (152)
32 The Avon Longitudinal Study of Parents and Children NC_000003.11 - 120352080 Oct 12, 2018 (152)
33 Genetic variation in the Estonian population NC_000003.11 - 120352080 Oct 12, 2018 (152)
34 ExAC NC_000003.11 - 120352080 Oct 12, 2018 (152)
35 gnomAD - Genomes NC_000003.11 - 120352080 Jul 13, 2019 (153)
36 gnomAD - Exomes NC_000003.11 - 120352080 Jul 13, 2019 (153)
37 The PAGE Study NC_000003.12 - 120633233 Jul 13, 2019 (153)
38 TopMed NC_000003.12 - 120633233 Oct 12, 2018 (152)
39 UK 10K study - Twins NC_000003.11 - 120352080 Oct 12, 2018 (152)
40 ClinVar RCV000003323.9 Jul 13, 2019 (153)
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
17111800, 9531979, 6739176, 7094120, 46814607, 3075626, 9531979, ss342144220, ss488765863, ss491344684, ss780820711, ss783503128, ss1305859138, ss1608059109, ss1651053142, ss1687158206, ss1917771367, ss1946093441, ss1958598388, ss2021722790, ss2422577097, ss2733990156, ss2747077504, ss2798279091, ss2985267472, ss3628759117, ss3634913375, ss3640620674, ss3644826072, ss3654036544, ss3661000928, ss3744514704, ss3745213337 NC_000003.11:120352079:T:C NC_000003.12:120633232:T:C (self)
RCV000003323.9, 279878, 261518817, ss255605807, ss2255252641, ss3403596423, ss3771058409 NC_000003.12:120633232:T:C NC_000003.12:120633232:T:C (self)
Help

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

4 citations for rs120074173
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
10594001 Mutational analysis of the HGO gene in Finnish alkaptonuria patients. Beltrán-Valero de Bernabé D et al. 1999 Journal of medical genetics
20301627 Alkaptonuria Introne WJ et al. 1993 GeneReviews®
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

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