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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.

rs2075504

Current Build 154

Released April 21, 2020

Organism
Homo sapiens
Position
chr3:120644528 (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 / T>C
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.02004 (629/31388, GnomAD)
C=0.0733 (367/5008, 1000G)
C=0.0031 (14/4480, Estonian) (+ 9 more)
C=0.0010 (4/3854, ALSPAC)
C=0.0011 (4/3708, TWINSUK)
C=0.2710 (794/2930, KOREAN)
C=0.023 (14/600, NorthernSweden)
C=0.005 (1/216, Qatari)
C=0.325 (69/212, Vietnamese)
T=0.43 (31/72, SGDP_PRJ)
T=0.4 (3/8, Siberian)
C=0.00515 (86/16702, ALFA Project)
Clinical Significance
Reported in ClinVar
Gene : Consequence
HGD : Intron Variant
Publications
0 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.120644528T>A
GRCh38.p12 chr 3 NC_000003.12:g.120644528T>C
GRCh37.p13 chr 3 NC_000003.11:g.120363375T>A
GRCh37.p13 chr 3 NC_000003.11:g.120363375T>C
HGD RefSeqGene NG_011957.1:g.42954A>T
HGD RefSeqGene NG_011957.1:g.42954A>G
Gene: HGD, homogentisate 1,2-dioxygenase (minus strand)
Molecule type Change Amino acid[Codon] SO Term
HGD transcript NM_000187.4:c.650-85A>T N/A Intron Variant
HGD transcript variant X1 XM_005247412.2:c.549+2445…

XM_005247412.2:c.549+2445A>T

N/A Intron Variant
HGD transcript variant X2 XM_005247413.2:c.650-85A>T N/A Intron Variant
HGD transcript variant X4 XM_011512746.2:c.650-85A>T N/A Intron Variant
HGD transcript variant X3 XM_017006277.2:c.227-85A>T N/A Intron Variant
HGD transcript variant X5 XM_005247414.5:c.*39= N/A 3 Prime UTR 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: 779013 )
ClinVar Accession Disease Names Clinical Significance
RCV000967303.1 not provided Benign

ALFA Allele Frequency (New)
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 16702 T=0.99485 C=0.00515
European Sub 12214 T=0.99812 C=0.00188
African Sub 2864 T=0.9986 C=0.0014
African Others Sub 108 T=1.000 C=0.000
African American Sub 2756 T=0.9985 C=0.0015
Asian Sub 108 T=0.648 C=0.352
East Asian Sub 84 T=0.64 C=0.36
Other Asian Sub 24 T=0.67 C=0.33
Latin American 1 Sub 146 T=1.000 C=0.000
Latin American 2 Sub 610 T=0.997 C=0.003
South Asian Sub 94 T=0.97 C=0.03
Other Sub 666 T=0.976 C=0.024


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 - Genomes Global Study-wide 31388 T=0.97996 C=0.02004
gnomAD - Genomes European Sub 18910 T=0.99593 C=0.00407
gnomAD - Genomes African Sub 8710 T=0.9971 C=0.0029
gnomAD - Genomes East Asian Sub 1542 T=0.6738 C=0.3262
gnomAD - Genomes Other Sub 1088 T=0.9807 C=0.0193
gnomAD - Genomes American Sub 848 T=1.000 C=0.000
gnomAD - Genomes Ashkenazi Jewish Sub 290 T=0.990 C=0.010
1000Genomes Global Study-wide 5008 T=0.9267 C=0.0733
1000Genomes African Sub 1322 T=1.0000 C=0.0000
1000Genomes East Asian Sub 1008 T=0.6925 C=0.3075
1000Genomes Europe Sub 1006 T=0.9970 C=0.0030
1000Genomes South Asian Sub 978 T=0.946 C=0.054
1000Genomes American Sub 694 T=0.999 C=0.001
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.9969 C=0.0031
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.9990 C=0.0010
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.9989 C=0.0011
KOREAN population from KRGDB KOREAN Study-wide 2930 T=0.7290 A=0.0000, C=0.2710
Northern Sweden ACPOP Study-wide 600 T=0.977 C=0.023
Qatari Global Study-wide 216 T=0.995 C=0.005
A Vietnamese Genetic Variation Database Global Study-wide 212 T=0.675 C=0.325
SGDP_PRJ Global Study-wide 72 T=0.43 C=0.57
Siberian Global Study-wide 8 T=0.4 C=0.6
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 C
GRCh38.p12 chr 3 NC_000003.12:g.120644528= NC_000003.12:g.120644528T>A NC_000003.12:g.120644528T>C
GRCh37.p13 chr 3 NC_000003.11:g.120363375= NC_000003.11:g.120363375T>A NC_000003.11:g.120363375T>C
HGD RefSeqGene NG_011957.1:g.42954= NG_011957.1:g.42954A>T NG_011957.1:g.42954A>G
HGD transcript variant X5 XM_005247414.5:c.*39= XM_005247414.5:c.*39A>T XM_005247414.5:c.*39A>G
HGD transcript variant X3 XM_005247414.1:c.*39= XM_005247414.1:c.*39A>T XM_005247414.1:c.*39A>G
HGD transcript NM_000187.3:c.650-85= NM_000187.3:c.650-85A>T NM_000187.3:c.650-85A>G
HGD transcript NM_000187.4:c.650-85= NM_000187.4:c.650-85A>T NM_000187.4:c.650-85A>G
HGD transcript variant X1 XM_005247412.1:c.549+2445= XM_005247412.1:c.549+2445A>T XM_005247412.1:c.549+2445A>G
HGD transcript variant X1 XM_005247412.2:c.549+2445= XM_005247412.2:c.549+2445A>T XM_005247412.2:c.549+2445A>G
HGD transcript variant X2 XM_005247413.1:c.650-85= XM_005247413.1:c.650-85A>T XM_005247413.1:c.650-85A>G
HGD transcript variant X2 XM_005247413.2:c.650-85= XM_005247413.2:c.650-85A>T XM_005247413.2:c.650-85A>G
HGD transcript variant X4 XM_011512746.2:c.650-85= XM_011512746.2:c.650-85A>T XM_011512746.2:c.650-85A>G
HGD transcript variant X3 XM_017006277.2:c.227-85= XM_017006277.2:c.227-85A>T XM_017006277.2:c.227-85A>G
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, 11 Frequency, 1 ClinVar submissions
No Submitter Submission ID Date (Build)
1 YUSUKE ss2990582 Jun 15, 2001 (96)
2 HGBASE ss3184332 Aug 15, 2001 (98)
3 BGI ss103978155 Dec 01, 2009 (131)
4 GMI ss156111222 Dec 01, 2009 (131)
5 GMI ss277320336 May 04, 2012 (137)
6 1000GENOMES ss331004696 May 09, 2011 (134)
7 SSMP ss650611994 Apr 25, 2013 (138)
8 JMKIDD_LAB ss1070777223 Aug 21, 2014 (142)
9 1000GENOMES ss1305859450 Aug 21, 2014 (142)
10 EVA_DECODE ss1588565940 Apr 01, 2015 (144)
11 EVA_UK10K_ALSPAC ss1608059293 Apr 01, 2015 (144)
12 EVA_UK10K_TWINSUK ss1651053326 Apr 01, 2015 (144)
13 WEILL_CORNELL_DGM ss1922310056 Feb 12, 2016 (147)
14 JJLAB ss2021722832 Sep 14, 2016 (149)
15 USC_VALOUEV ss2149814965 Dec 20, 2016 (150)
16 HUMAN_LONGEVITY ss2255253285 Dec 20, 2016 (150)
17 TOPMED ss2422577709 Dec 20, 2016 (150)
18 SYSTEMSBIOZJU ss2625363266 Nov 08, 2017 (151)
19 GRF ss2705218289 Nov 08, 2017 (151)
20 GNOMAD ss2798279893 Nov 08, 2017 (151)
21 SWEGEN ss2993074340 Nov 08, 2017 (151)
22 TOPMED ss3403598356 Nov 08, 2017 (151)
23 OMUKHERJEE_ADBS ss3646291542 Oct 12, 2018 (152)
24 EGCUT_WGS ss3661001054 Jul 13, 2019 (153)
25 EVA_DECODE ss3710145382 Jul 13, 2019 (153)
26 ACPOP ss3730286678 Jul 13, 2019 (153)
27 EVA ss3760599293 Jul 13, 2019 (153)
28 KHV_HUMAN_GENOMES ss3803735579 Jul 13, 2019 (153)
29 SGDP_PRJ ss3856813861 Apr 25, 2020 (154)
30 KRGDB ss3902806395 Apr 25, 2020 (154)
31 1000Genomes NC_000003.11 - 120363375 Oct 12, 2018 (152)
32 The Avon Longitudinal Study of Parents and Children NC_000003.11 - 120363375 Oct 12, 2018 (152)
33 Genetic variation in the Estonian population NC_000003.11 - 120363375 Oct 12, 2018 (152)
34 gnomAD - Genomes NC_000003.11 - 120363375 Jul 13, 2019 (153)
35 KOREAN population from KRGDB NC_000003.11 - 120363375 Apr 25, 2020 (154)
36 Northern Sweden NC_000003.11 - 120363375 Jul 13, 2019 (153)
37 Qatari NC_000003.11 - 120363375 Apr 25, 2020 (154)
38 SGDP_PRJ NC_000003.11 - 120363375 Apr 25, 2020 (154)
39 Siberian NC_000003.11 - 120363375 Apr 25, 2020 (154)
40 UK 10K study - Twins NC_000003.11 - 120363375 Oct 12, 2018 (152)
41 A Vietnamese Genetic Variation Database NC_000003.11 - 120363375 Jul 13, 2019 (153)
42 ClinVar RCV000967303.1 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
9983789, ss3902806395 NC_000003.11:120363374:T:A NC_000003.12:120644527:T:A
ss277320336, ss1588565940 NC_000003.10:121846064:T:C NC_000003.12:120644527:T:C (self)
17112123, 9532180, 6739302, 46815410, 9983789, 3571543, 4351986, 8830841, 2331319, 9532180, 2077901, ss331004696, ss650611994, ss1070777223, ss1305859450, ss1608059293, ss1651053326, ss1922310056, ss2021722832, ss2149814965, ss2422577709, ss2625363266, ss2705218289, ss2798279893, ss2993074340, ss3646291542, ss3661001054, ss3730286678, ss3760599293, ss3856813861, ss3902806395 NC_000003.11:120363374:T:C NC_000003.12:120644527:T:C (self)
RCV000967303.1, ss2255253285, ss3403598356, ss3710145382, ss3803735579 NC_000003.12:120644527:T:C NC_000003.12:120644527:T:C (self)
ss2990582, ss3184332, ss103978155, ss156111222 NT_005612.16:26858520:T:C NC_000003.12:120644527: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.

No publications for rs2075504

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.post557+f76c771