Skip to main page content
Accesskeys

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.

rs1800722

Current Build 153

Released July 9, 2019

Organism
Homo sapiens
Position
chr3:120670396 (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=0.02033 (5104/251080, GnomAD_exome)
C=0.02012 (2526/125568, TOPMED)
C=0.02110 (2554/121060, ExAC) (+ 7 more)
C=0.0191 (600/31402, GnomAD)
C=0.0240 (312/12998, GO-ESP)
C=0.011 (54/5008, 1000G)
C=0.022 (99/4480, Estonian)
C=0.035 (135/3854, ALSPAC)
C=0.031 (114/3708, TWINSUK)
C=0.04 (23/600, NorthernSweden)
Clinical Significance
Not 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.120670396T>C
GRCh37.p13 chr 3 NC_000003.11:g.120389243T>C
HGD RefSeqGene NG_011957.1:g.17086A>G
Gene: HGD, homogentisate 1,2-dioxygenase (minus strand)
Molecule type Change Amino acid[Codon] SO Term
HGD transcript NM_000187.4:c. N/A Intron Variant
HGD transcript variant X1 XM_005247412.2:c. N/A Intron Variant
HGD transcript variant X2 XM_005247413.2:c. N/A Intron Variant
HGD transcript variant X5 XM_005247414.5:c. N/A Intron Variant
HGD transcript variant X4 XM_011512746.2:c. N/A Intron Variant
HGD transcript variant X3 XM_017006277.2:c. N/A Intron 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.

Not Reported in ClinVar
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 251080 T=0.97967 C=0.02033
gnomAD - Exomes European Sub 135180 T=0.97116 C=0.02884
gnomAD - Exomes Asian Sub 48978 T=0.9906 C=0.0094
gnomAD - Exomes American Sub 34482 T=0.9868 C=0.0132
gnomAD - Exomes African Sub 16246 T=0.9956 C=0.0044
gnomAD - Exomes Ashkenazi Jewish Sub 10072 T=0.9905 C=0.0095
gnomAD - Exomes Other Sub 6122 T=0.980 C=0.020
TopMed Global Study-wide 125568 T=0.97988 C=0.02012
ExAC Global Study-wide 121060 T=0.97890 C=0.02110
ExAC Europe Sub 73226 T=0.9713 C=0.0287
ExAC Asian Sub 25104 T=0.9899 C=0.0101
ExAC American Sub 11430 T=0.9881 C=0.0119
ExAC African Sub 10396 T=0.9954 C=0.0046
ExAC Other Sub 904 T=0.98 C=0.02
gnomAD - Genomes Global Study-wide 31402 T=0.9809 C=0.0191
gnomAD - Genomes European Sub 18902 T=0.9733 C=0.0267
gnomAD - Genomes African Sub 8714 T=0.993 C=0.007
gnomAD - Genomes East Asian Sub 1560 T=1.000 C=0.000
gnomAD - Genomes Other Sub 1088 T=0.983 C=0.017
gnomAD - Genomes American Sub 848 T=0.99 C=0.01
gnomAD - Genomes Ashkenazi Jewish Sub 290 T=0.99 C=0.01
GO Exome Sequencing Project Global Study-wide 12998 T=0.9760 C=0.0240
GO Exome Sequencing Project European American Sub 8592 T=0.967 C=0.033
GO Exome Sequencing Project African American Sub 4406 T=0.993 C=0.007
1000Genomes Global Study-wide 5008 T=0.989 C=0.011
1000Genomes African Sub 1322 T=0.999 C=0.001
1000Genomes East Asian Sub 1008 T=1.000 C=0.000
1000Genomes Europe Sub 1006 T=0.973 C=0.027
1000Genomes South Asian Sub 978 T=0.98 C=0.02
1000Genomes American Sub 694 T=0.99 C=0.01
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.978 C=0.022
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.965 C=0.035
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.969 C=0.031
Northern Sweden ACPOP Study-wide 600 T=0.96 C=0.04
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.120670396= NC_000003.12:g.12067039...

NC_000003.12:g.120670396T>C

GRCh37.p13 chr 3 NC_000003.11:g.120389243= NC_000003.11:g.12038924...

NC_000003.11:g.120389243T>C

HGD RefSeqGene NG_011957.1:g.17086= NG_011957.1:g.17086A>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, 10 Frequency submissions
No Submitter Submission ID Date (Build)
1 HGBASE ss2420847 Nov 14, 2000 (89)
2 1000GENOMES ss331004973 May 09, 2011 (134)
3 1000GENOMES ss489894714 May 04, 2012 (137)
4 ILLUMINA ss535075567 Sep 08, 2015 (146)
5 NHLBI-ESP ss712547065 Apr 25, 2013 (138)
6 EVA-GONL ss979083940 Aug 21, 2014 (142)
7 JMKIDD_LAB ss1070777391 Aug 21, 2014 (142)
8 1000GENOMES ss1305860179 Aug 21, 2014 (142)
9 DDI ss1429564117 Apr 01, 2015 (144)
10 EVA_GENOME_DK ss1580152578 Apr 01, 2015 (144)
11 EVA_DECODE ss1588566159 Apr 01, 2015 (144)
12 EVA_UK10K_ALSPAC ss1608059708 Apr 01, 2015 (144)
13 EVA_UK10K_TWINSUK ss1651053741 Apr 01, 2015 (144)
14 EVA_EXAC ss1687158513 Apr 01, 2015 (144)
15 EVA_MGP ss1711029904 Apr 01, 2015 (144)
16 WEILL_CORNELL_DGM ss1922310268 Feb 12, 2016 (147)
17 JJLAB ss2021722971 Sep 14, 2016 (149)
18 HUMAN_LONGEVITY ss2255254797 Dec 20, 2016 (150)
19 TOPMED ss2422579229 Dec 20, 2016 (150)
20 GNOMAD ss2733990622 Nov 08, 2017 (151)
21 GNOMAD ss2747077630 Nov 08, 2017 (151)
22 GNOMAD ss2798281788 Nov 08, 2017 (151)
23 SWEGEN ss2993074626 Nov 08, 2017 (151)
24 TOPMED ss3403602851 Nov 08, 2017 (151)
25 ILLUMINA ss3628759187 Oct 12, 2018 (152)
26 BIOINF_KMB_FNS_UNIBA ss3645739068 Oct 12, 2018 (152)
27 EGCUT_WGS ss3661001388 Jul 13, 2019 (153)
28 EVA_DECODE ss3710145729 Jul 13, 2019 (153)
29 ACPOP ss3730286855 Jul 13, 2019 (153)
30 KHV_HUMAN_GENOMES ss3803735804 Jul 13, 2019 (153)
31 1000Genomes NC_000003.11 - 120389243 Oct 12, 2018 (152)
32 The Avon Longitudinal Study of Parents and Children NC_000003.11 - 120389243 Oct 12, 2018 (152)
33 Genetic variation in the Estonian population NC_000003.11 - 120389243 Oct 12, 2018 (152)
34 ExAC NC_000003.11 - 120389243 Oct 12, 2018 (152)
35 gnomAD - Genomes NC_000003.11 - 120389243 Jul 13, 2019 (153)
36 gnomAD - Exomes NC_000003.11 - 120389243 Jul 13, 2019 (153)
37 GO Exome Sequencing Project NC_000003.11 - 120389243 Oct 12, 2018 (152)
38 Northern Sweden NC_000003.11 - 120389243 Jul 13, 2019 (153)
39 TopMed NC_000003.12 - 120670396 Oct 12, 2018 (152)
40 UK 10K study - Twins NC_000003.11 - 120389243 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).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss1588566159 NC_000003.10:121871932:T:C NC_000003.12:120670395:T:C (self)
17112874, 9532632, 6739636, 7094445, 46817339, 3076120, 403766, 3571720, 9532632, ss331004973, ss489894714, ss535075567, ss712547065, ss979083940, ss1070777391, ss1305860179, ss1429564117, ss1580152578, ss1608059708, ss1651053741, ss1687158513, ss1711029904, ss1922310268, ss2021722971, ss2422579229, ss2733990622, ss2747077630, ss2798281788, ss2993074626, ss3628759187, ss3661001388, ss3730286855 NC_000003.11:120389242:T:C NC_000003.12:120670395:T:C (self)
261524227, ss2255254797, ss3403602851, ss3645739068, ss3710145729, ss3803735804 NC_000003.12:120670395:T:C NC_000003.12:120670395:T:C (self)
ss2420847 NT_005612.16:26884388:T:C NC_000003.12:120670395: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 rs1800722

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