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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.

rs804974

Current Build 153

Released July 9, 2019

Organism
Homo sapiens
Position
chr3:120632944 (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
C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.24923 (31295/125568, TOPMED)
T=0.2332 (7301/31302, GnomAD)
T=0.218 (1092/5008, 1000G) (+ 5 more)
T=0.141 (631/4480, Estonian)
T=0.203 (783/3854, ALSPAC)
T=0.211 (781/3708, TWINSUK)
T=0.18 (106/600, NorthernSweden)
T=0.06 (12/214, Vietnamese)
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.120632944C>T
GRCh37.p13 chr 3 NC_000003.11:g.120351791C>T
HGD RefSeqGene NG_011957.1:g.54538G>A
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 X3 XM_017006277.2:c. N/A Intron 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
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
TopMed Global Study-wide 125568 C=0.75077 T=0.24923
gnomAD - Genomes Global Study-wide 31302 C=0.7668 T=0.2332
gnomAD - Genomes European Sub 18866 C=0.8305 T=0.1695
gnomAD - Genomes African Sub 8656 C=0.570 T=0.430
gnomAD - Genomes East Asian Sub 1556 C=0.959 T=0.041
gnomAD - Genomes Other Sub 1086 C=0.842 T=0.158
gnomAD - Genomes American Sub 848 C=0.87 T=0.13
gnomAD - Genomes Ashkenazi Jewish Sub 290 C=0.86 T=0.14
1000Genomes Global Study-wide 5008 C=0.782 T=0.218
1000Genomes African Sub 1322 C=0.533 T=0.467
1000Genomes East Asian Sub 1008 C=0.964 T=0.036
1000Genomes Europe Sub 1006 C=0.838 T=0.162
1000Genomes South Asian Sub 978 C=0.83 T=0.17
1000Genomes American Sub 694 C=0.84 T=0.16
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.859 T=0.141
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.797 T=0.203
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.789 T=0.211
Northern Sweden ACPOP Study-wide 600 C=0.82 T=0.18
A Vietnamese Genetic Variation Database Global Study-wide 214 C=0.94 T=0.06
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= T Note
GRCh38.p12 chr 3 NC_000003.12:g.120632944= NC_000003.12:g.12063294...

NC_000003.12:g.120632944C>T

GRCh37.p13 chr 3 NC_000003.11:g.120351791= NC_000003.11:g.12035179...

NC_000003.11:g.120351791C>T

HGD RefSeqGene NG_011957.1:g.54538= NG_011957.1:g.54538G>A
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#.

53 SubSNP, 8 Frequency submissions
No Submitter Submission ID Date (Build)
1 KWOK ss1028912 Oct 05, 2000 (86)
2 KWOK ss1964995 Oct 18, 2000 (87)
3 SC_JCM ss3621052 Sep 28, 2001 (100)
4 ABI ss41997237 Mar 14, 2006 (126)
5 AFFY ss66100083 Dec 02, 2006 (127)
6 AFFY ss76065883 Dec 06, 2007 (129)
7 KRIBB_YJKIM ss81438855 Dec 15, 2007 (131)
8 BCMHGSC_JDW ss92257317 Mar 23, 2008 (129)
9 ENSEMBL ss143193567 Dec 01, 2009 (131)
10 GMI ss156111132 Dec 01, 2009 (131)
11 COMPLETE_GENOMICS ss162547488 Jul 04, 2010 (132)
12 COMPLETE_GENOMICS ss164110576 Jul 04, 2010 (132)
13 AFFY ss172379559 Jul 04, 2010 (132)
14 BUSHMAN ss203091181 Jul 04, 2010 (132)
15 1000GENOMES ss232003915 Jul 14, 2010 (132)
16 GMI ss277320305 May 04, 2012 (137)
17 GMI ss284734874 Apr 25, 2013 (138)
18 PJP ss292898974 May 09, 2011 (134)
19 TISHKOFF ss556900073 Apr 25, 2013 (138)
20 SSMP ss650611959 Apr 25, 2013 (138)
21 EVA-GONL ss979083650 Aug 21, 2014 (142)
22 JMKIDD_LAB ss1070777171 Aug 21, 2014 (142)
23 1000GENOMES ss1305859125 Aug 21, 2014 (142)
24 HAMMER_LAB ss1397350241 Sep 08, 2015 (146)
25 DDI ss1429564013 Apr 01, 2015 (144)
26 EVA_GENOME_DK ss1580152431 Apr 01, 2015 (144)
27 EVA_DECODE ss1588565856 Apr 01, 2015 (144)
28 EVA_UK10K_ALSPAC ss1608059104 Apr 01, 2015 (144)
29 EVA_UK10K_TWINSUK ss1651053137 Apr 01, 2015 (144)
30 EVA_SVP ss1712606991 Apr 01, 2015 (144)
31 HAMMER_LAB ss1799930554 Sep 08, 2015 (146)
32 WEILL_CORNELL_DGM ss1922309988 Feb 12, 2016 (147)
33 JJLAB ss2021722786 Sep 14, 2016 (149)
34 USC_VALOUEV ss2149814911 Dec 20, 2016 (150)
35 HUMAN_LONGEVITY ss2255252622 Dec 20, 2016 (150)
36 TOPMED ss2422577082 Dec 20, 2016 (150)
37 GRF ss2705218257 Nov 08, 2017 (151)
38 GNOMAD ss2798279068 Nov 08, 2017 (151)
39 AFFY ss2985267469 Nov 08, 2017 (151)
40 AFFY ss2985890759 Nov 08, 2017 (151)
41 SWEGEN ss2993074219 Nov 08, 2017 (151)
42 BIOINF_KMB_FNS_UNIBA ss3024628210 Nov 08, 2017 (151)
43 CSHL ss3345231321 Nov 08, 2017 (151)
44 TOPMED ss3403596358 Nov 08, 2017 (151)
45 ILLUMINA ss3654036540 Oct 12, 2018 (152)
46 EGCUT_WGS ss3661000922 Jul 13, 2019 (153)
47 EVA_DECODE ss3710145233 Jul 13, 2019 (153)
48 ACPOP ss3730286619 Jul 13, 2019 (153)
49 EVA ss3760599198 Jul 13, 2019 (153)
50 PACBIO ss3784443257 Jul 13, 2019 (153)
51 PACBIO ss3789940715 Jul 13, 2019 (153)
52 PACBIO ss3794815150 Jul 13, 2019 (153)
53 KHV_HUMAN_GENOMES ss3803735490 Jul 13, 2019 (153)
54 1000Genomes NC_000003.11 - 120351791 Oct 12, 2018 (152)
55 The Avon Longitudinal Study of Parents and Children NC_000003.11 - 120351791 Oct 12, 2018 (152)
56 Genetic variation in the Estonian population NC_000003.11 - 120351791 Oct 12, 2018 (152)
57 gnomAD - Genomes NC_000003.11 - 120351791 Jul 13, 2019 (153)
58 Northern Sweden NC_000003.11 - 120351791 Jul 13, 2019 (153)
59 TopMed NC_000003.12 - 120632944 Oct 12, 2018 (152)
60 UK 10K study - Twins NC_000003.11 - 120351791 Oct 12, 2018 (152)
61 A Vietnamese Genetic Variation Database NC_000003.11 - 120351791 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).

Associated ID History Updated (Build)
rs35208197 May 23, 2006 (127)
rs60790503 Dec 02, 2009 (131)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss66100083, ss76065883, ss92257317, ss162547488, ss164110576, ss172379559, ss203091181, ss277320305, ss284734874, ss292898974, ss1397350241, ss1588565856, ss1712606991 NC_000003.10:121834480:C:T NC_000003.12:120632943:C:T (self)
17111787, 9531974, 6739170, 46814584, 3571484, 9531974, 2077853, ss232003915, ss556900073, ss650611959, ss979083650, ss1070777171, ss1305859125, ss1429564013, ss1580152431, ss1608059104, ss1651053137, ss1799930554, ss1922309988, ss2021722786, ss2149814911, ss2422577082, ss2705218257, ss2798279068, ss2985267469, ss2985890759, ss2993074219, ss3345231321, ss3654036540, ss3661000922, ss3730286619, ss3760599198, ss3784443257, ss3789940715, ss3794815150 NC_000003.11:120351790:C:T NC_000003.12:120632943:C:T (self)
261518757, ss2255252622, ss3024628210, ss3403596358, ss3710145233, ss3803735490 NC_000003.12:120632943:C:T NC_000003.12:120632943:C:T (self)
ss1028912, ss1964995, ss3621052, ss41997237, ss81438855, ss143193567, ss156111132 NT_005612.16:26846936:C:T NC_000003.12:120632943: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.

No publications for rs804974

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