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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.

rs120074174

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr3:120641660 (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.

Alleles
C>A / C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.000056 (14/251412, GnomAD_exome)
T=0.000057 (8/140234, GnomAD)
T=0.000040 (5/124920, ALFA) (+ 2 more)
T=0.000074 (9/121386, ExAC)
T=0.00013 (10/78700, PAGE_STUDY)
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.p13 chr 3 NC_000003.12:g.120641660C>A
GRCh38.p13 chr 3 NC_000003.12:g.120641660C>T
GRCh37.p13 chr 3 NC_000003.11:g.120360507C>A
GRCh37.p13 chr 3 NC_000003.11:g.120360507C>T
HGD RefSeqGene NG_011957.1:g.45822G>T
HGD RefSeqGene NG_011957.1:g.45822G>A
Gene: HGD, homogentisate 1,2-dioxygenase (minus strand)
Molecule type Change Amino acid[Codon] SO Term
HGD transcript NM_000187.4:c.808G>T G [GGG] > W [TGG] Coding Sequence Variant
homogentisate 1,2-dioxygenase NP_000178.2:p.Gly270Trp G (Gly) > W (Trp) Missense Variant
HGD transcript NM_000187.4:c.808G>A G [GGG] > R [AGG] Coding Sequence Variant
homogentisate 1,2-dioxygenase NP_000178.2:p.Gly270Arg G (Gly) > R (Arg) Missense Variant
HGD transcript variant X5 XM_005247414.5:c. N/A Genic Downstream Transcript Variant
HGD transcript variant X1 XM_005247412.2:c.583G>T G [GGG] > W [TGG] Coding Sequence Variant
homogentisate 1,2-dioxygenase isoform X1 XP_005247469.1:p.Gly195Trp G (Gly) > W (Trp) Missense Variant
HGD transcript variant X1 XM_005247412.2:c.583G>A G [GGG] > R [AGG] Coding Sequence Variant
homogentisate 1,2-dioxygenase isoform X1 XP_005247469.1:p.Gly195Arg G (Gly) > R (Arg) Missense Variant
HGD transcript variant X2 XM_005247413.2:c.808G>T G [GGG] > W [TGG] Coding Sequence Variant
homogentisate 1,2-dioxygenase isoform X2 XP_005247470.1:p.Gly270Trp G (Gly) > W (Trp) Missense Variant
HGD transcript variant X2 XM_005247413.2:c.808G>A G [GGG] > R [AGG] Coding Sequence Variant
homogentisate 1,2-dioxygenase isoform X2 XP_005247470.1:p.Gly270Arg G (Gly) > R (Arg) Missense Variant
HGD transcript variant X3 XM_017006277.2:c.385G>T G [GGG] > W [TGG] Coding Sequence Variant
homogentisate 1,2-dioxygenase isoform X3 XP_016861766.1:p.Gly129Trp G (Gly) > W (Trp) Missense Variant
HGD transcript variant X3 XM_017006277.2:c.385G>A G [GGG] > R [AGG] Coding Sequence Variant
homogentisate 1,2-dioxygenase isoform X3 XP_016861766.1:p.Gly129Arg G (Gly) > R (Arg) Missense Variant
HGD transcript variant X4 XM_011512746.2:c.808G>T G [GGG] > W [TGG] Coding Sequence Variant
homogentisate 1,2-dioxygenase isoform X4 XP_011511048.1:p.Gly270Trp G (Gly) > W (Trp) Missense Variant
HGD transcript variant X4 XM_011512746.2:c.808G>A G [GGG] > R [AGG] Coding Sequence Variant
homogentisate 1,2-dioxygenase isoform X4 XP_011511048.1:p.Gly270Arg G (Gly) > R (Arg) 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: T (allele ID: 18214 )
ClinVar Accession Disease Names Clinical Significance
RCV000003325.5 Alkaptonuria Pathogenic

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 124920 C=0.999960 A=0.000000, T=0.000040
European Sub 109716 C=0.999982 A=0.000000, T=0.000018
African Sub 3778 C=1.0000 A=0.0000, T=0.0000
African Others Sub 168 C=1.000 A=0.000, T=0.000
African American Sub 3610 C=1.0000 A=0.0000, T=0.0000
Asian Sub 3308 C=1.0000 A=0.0000, T=0.0000
East Asian Sub 2682 C=1.0000 A=0.0000, T=0.0000
Other Asian Sub 626 C=1.000 A=0.000, T=0.000
Latin American 1 Sub 790 C=0.996 A=0.000, T=0.004
Latin American 2 Sub 946 C=1.000 A=0.000, T=0.000
South Asian Sub 280 C=1.000 A=0.000, T=0.000
Other Sub 6102 C=1.0000 A=0.0000, T=0.0000


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 251412 C=0.999944 T=0.000056
gnomAD - Exomes European Sub 135344 C=0.999970 T=0.000030
gnomAD - Exomes Asian Sub 49008 C=0.99988 T=0.00012
gnomAD - Exomes American Sub 34590 C=0.99997 T=0.00003
gnomAD - Exomes African Sub 16256 C=0.99982 T=0.00018
gnomAD - Exomes Ashkenazi Jewish Sub 10078 C=1.00000 T=0.00000
gnomAD - Exomes Other Sub 6136 C=1.0000 T=0.0000
gnomAD - Genomes Global Study-wide 140234 C=0.999943 T=0.000057
gnomAD - Genomes European Sub 75946 C=1.00000 T=0.00000
gnomAD - Genomes African Sub 42020 C=0.99981 T=0.00019
gnomAD - Genomes American Sub 13658 C=1.00000 T=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3324 C=1.0000 T=0.0000
gnomAD - Genomes East Asian Sub 3132 C=1.0000 T=0.0000
gnomAD - Genomes Other Sub 2154 C=1.0000 T=0.0000
ExAC Global Study-wide 121386 C=0.999926 T=0.000074
ExAC Europe Sub 73344 C=0.99997 T=0.00003
ExAC Asian Sub 25160 C=0.99984 T=0.00016
ExAC American Sub 11568 C=0.99991 T=0.00009
ExAC African Sub 10406 C=0.99981 T=0.00019
ExAC Other Sub 908 C=1.000 T=0.000
The PAGE Study Global Study-wide 78700 C=0.99987 T=0.00013
The PAGE Study AfricanAmerican Sub 32516 C=0.99975 T=0.00025
The PAGE Study Mexican Sub 10810 C=1.00000 T=0.00000
The PAGE Study Asian Sub 8318 C=1.0000 T=0.0000
The PAGE Study PuertoRican Sub 7916 C=1.0000 T=0.0000
The PAGE Study NativeHawaiian Sub 4534 C=1.0000 T=0.0000
The PAGE Study Cuban Sub 4230 C=1.0000 T=0.0000
The PAGE Study Dominican Sub 3828 C=0.9995 T=0.0005
The PAGE Study CentralAmerican Sub 2450 C=1.0000 T=0.0000
The PAGE Study SouthAmerican Sub 1982 C=1.0000 T=0.0000
The PAGE Study NativeAmerican Sub 1260 C=1.0000 T=0.0000
The PAGE Study SouthAsian Sub 856 C=1.000 T=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 C= A T
GRCh38.p13 chr 3 NC_000003.12:g.120641660= NC_000003.12:g.120641660C>A NC_000003.12:g.120641660C>T
GRCh37.p13 chr 3 NC_000003.11:g.120360507= NC_000003.11:g.120360507C>A NC_000003.11:g.120360507C>T
HGD RefSeqGene NG_011957.1:g.45822= NG_011957.1:g.45822G>T NG_011957.1:g.45822G>A
HGD transcript NM_000187.4:c.808= NM_000187.4:c.808G>T NM_000187.4:c.808G>A
HGD transcript NM_000187.3:c.808= NM_000187.3:c.808G>T NM_000187.3:c.808G>A
HGD transcript variant X3 XM_017006277.2:c.385= XM_017006277.2:c.385G>T XM_017006277.2:c.385G>A
HGD transcript variant X1 XM_005247412.2:c.583= XM_005247412.2:c.583G>T XM_005247412.2:c.583G>A
HGD transcript variant X1 XM_005247412.1:c.583= XM_005247412.1:c.583G>T XM_005247412.1:c.583G>A
HGD transcript variant X2 XM_005247413.2:c.808= XM_005247413.2:c.808G>T XM_005247413.2:c.808G>A
HGD transcript variant X2 XM_005247413.1:c.808= XM_005247413.1:c.808G>T XM_005247413.1:c.808G>A
HGD transcript variant X4 XM_011512746.2:c.808= XM_011512746.2:c.808G>T XM_011512746.2:c.808G>A
homogentisate 1,2-dioxygenase NP_000178.2:p.Gly270= NP_000178.2:p.Gly270Trp NP_000178.2:p.Gly270Arg
homogentisate 1,2-dioxygenase isoform X3 XP_016861766.1:p.Gly129= XP_016861766.1:p.Gly129Trp XP_016861766.1:p.Gly129Arg
homogentisate 1,2-dioxygenase isoform X1 XP_005247469.1:p.Gly195= XP_005247469.1:p.Gly195Trp XP_005247469.1:p.Gly195Arg
homogentisate 1,2-dioxygenase isoform X2 XP_005247470.1:p.Gly270= XP_005247470.1:p.Gly270Trp XP_005247470.1:p.Gly270Arg
homogentisate 1,2-dioxygenase isoform X4 XP_011511048.1:p.Gly270= XP_011511048.1:p.Gly270Trp XP_011511048.1:p.Gly270Arg
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#.

24 SubSNP, 7 Frequency, 1 ClinVar submissions
No Submitter Submission ID Date (Build)
1 OMIM-CURATED-RECORDS ss255605811 Aug 20, 2010 (132)
2 NHLBI-ESP ss342144225 May 09, 2011 (134)
3 EVA_EXAC ss1687158291 Apr 01, 2015 (144)
4 ILLUMINA ss1946093447 Feb 12, 2016 (147)
5 ILLUMINA ss1958598399 Feb 12, 2016 (147)
6 TOPMED ss2422577566 Dec 20, 2016 (150)
7 TOPMED ss2422577567 Dec 20, 2016 (150)
8 GNOMAD ss2733990301 Nov 08, 2017 (151)
9 GNOMAD ss2747077547 Nov 08, 2017 (151)
10 GNOMAD ss2798279690 Nov 08, 2017 (151)
11 AFFY ss2985267481 Nov 08, 2017 (151)
12 ILLUMINA ss3022278757 Nov 08, 2017 (151)
13 TOPMED ss3403597891 Nov 08, 2017 (151)
14 TOPMED ss3403597892 Nov 08, 2017 (151)
15 ILLUMINA ss3625824234 Oct 12, 2018 (152)
16 ILLUMINA ss3644826078 Oct 12, 2018 (152)
17 ILLUMINA ss3652757280 Oct 12, 2018 (152)
18 ILLUMINA ss3654036553 Oct 12, 2018 (152)
19 ILLUMINA ss3726050075 Jul 13, 2019 (153)
20 ILLUMINA ss3744221075 Jul 13, 2019 (153)
21 PAGE_CC ss3771058419 Jul 13, 2019 (153)
22 EVA ss3823945407 Apr 25, 2020 (154)
23 TOPMED ss4581090827 Apr 26, 2021 (155)
24 TOPMED ss4581090828 Apr 26, 2021 (155)
25 ExAC NC_000003.11 - 120360507 Oct 12, 2018 (152)
26 gnomAD - Genomes NC_000003.12 - 120641660 Apr 26, 2021 (155)
27 gnomAD - Exomes NC_000003.11 - 120360507 Jul 13, 2019 (153)
28 The PAGE Study NC_000003.12 - 120641660 Jul 13, 2019 (153)
29 TopMed

Submission ignored due to conflicting rows:
Row 418468382 (NC_000003.12:120641659:C:A 3/264690)
Row 418468383 (NC_000003.12:120641659:C:T 29/264690)

- Apr 26, 2021 (155)
30 TopMed

Submission ignored due to conflicting rows:
Row 418468382 (NC_000003.12:120641659:C:A 3/264690)
Row 418468383 (NC_000003.12:120641659:C:T 29/264690)

- Apr 26, 2021 (155)
31 ALFA NC_000003.12 - 120641660 Apr 26, 2021 (155)
32 ClinVar RCV000003325.5 Apr 25, 2020 (154)
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
ss2422577566 NC_000003.11:120360506:C:A NC_000003.12:120641659:C:A (self)
261520013, 10669752737, ss3403597891, ss4581090827 NC_000003.12:120641659:C:A NC_000003.12:120641659:C:A (self)
7094209, 3075772, ss342144225, ss1687158291, ss1946093447, ss1958598399, ss2422577567, ss2733990301, ss2747077547, ss2798279690, ss2985267481, ss3022278757, ss3625824234, ss3644826078, ss3652757280, ss3654036553, ss3744221075, ss3823945407 NC_000003.11:120360506:C:T NC_000003.12:120641659:C:T (self)
RCV000003325.5, 121665114, 279888, 261520013, 10669752737, ss255605811, ss3403597892, ss3726050075, ss3771058419, ss4581090828 NC_000003.12:120641659:C:T NC_000003.12:120641659:C:T (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 rs120074174
PMID Title Author Year Journal
10482952 Allelic heterogeneity of alkaptonuria in Central Europe. Müller CR et al. 1999 European journal of human genetics
11001939 Structural and functional analysis of mutations in alkaptonuria. Rodríguez JM et al. 2000 Human molecular genetics
12872815 Alkaptonuria caused by compound heterozygote mutations. Elçioğlu NH et al. 2003 Genetic counseling (Geneva, Switzerland)
20301627 Alkaptonuria Introne WJ et al. 1993 GeneReviews®
Help

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.post596+ae089ad