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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.

rs17140396

Current Build 154

Released April 21, 2020

Organism
Homo sapiens
Position
chr3:120675674 (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=0.235092 (29520/125568, TOPMED)
C=0.23469 (7352/31326, GnomAD)
C=0.2111 (1057/5008, 1000G) (+ 15 more)
C=0.1853 (830/4480, Estonian)
C=0.2081 (802/3854, ALSPAC)
C=0.2203 (817/3708, TWINSUK)
C=0.2089 (758/3628, ALFA Project)
C=0.0038 (11/2922, KOREAN)
C=0.0049 (9/1832, Korea1K)
C=0.215 (215/998, GoNL)
C=0.193 (116/600, NorthernSweden)
C=0.212 (113/534, MGP)
C=0.148 (32/216, Qatari)
C=0.033 (7/210, Vietnamese)
T=0.454 (79/174, SGDP_PRJ)
C=0.28 (11/40, GENOME_DK)
T=0.5 (5/10, Siberian)
C=0.5 (5/10, Siberian)
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.120675674T>C
GRCh37.p13 chr 3 NC_000003.11:g.120394521T>C
HGD RefSeqGene NG_011957.1:g.11808A>G
Gene: HGD, homogentisate 1,2-dioxygenase (minus strand)
Molecule type Change Amino acid[Codon] SO Term
HGD transcript NM_000187.4:c.87+118A>G N/A Intron Variant
HGD transcript variant X1 XM_005247412.2:c.87+118A>G N/A Intron Variant
HGD transcript variant X2 XM_005247413.2:c.87+118A>G N/A Intron Variant
HGD transcript variant X5 XM_005247414.5:c.87+118A>G N/A Intron Variant
HGD transcript variant X4 XM_011512746.2:c.87+118A>G N/A Intron Variant
HGD transcript variant X3 XM_017006277.2:c.-337+118…

XM_017006277.2:c.-337+118A>G

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

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 30940 T=0.78655 C=0.21345
European Sub 24788 T=0.80253 C=0.19747
African Sub 3182 T=0.6499 C=0.3501
African Others Sub 124 T=0.621 C=0.379
African American Sub 3058 T=0.6511 C=0.3489
Asian Sub 128 T=0.977 C=0.023
East Asian Sub 100 T=0.99 C=0.01
Other Asian Sub 28 T=0.93 C=0.07
Latin American 1 Sub 168 T=0.815 C=0.185
Latin American 2 Sub 700 T=0.749 C=0.251
South Asian Sub 114 T=0.833 C=0.167
Other Sub 1860 T=0.8032 C=0.1968


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 T=0.764908 C=0.235092
gnomAD - Genomes Global Study-wide 31326 T=0.76531 C=0.23469
gnomAD - Genomes European Sub 18850 T=0.80202 C=0.19798
gnomAD - Genomes African Sub 8694 T=0.6403 C=0.3597
gnomAD - Genomes East Asian Sub 1558 T=0.9878 C=0.0122
gnomAD - Genomes Other Sub 1088 T=0.7932 C=0.2068
gnomAD - Genomes American Sub 846 T=0.755 C=0.245
gnomAD - Genomes Ashkenazi Jewish Sub 290 T=0.855 C=0.145
1000Genomes Global Study-wide 5008 T=0.7889 C=0.2111
1000Genomes African Sub 1322 T=0.5953 C=0.4047
1000Genomes East Asian Sub 1008 T=0.9891 C=0.0109
1000Genomes Europe Sub 1006 T=0.8091 C=0.1909
1000Genomes South Asian Sub 978 T=0.854 C=0.146
1000Genomes American Sub 694 T=0.746 C=0.254
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.8147 C=0.1853
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.7919 C=0.2081
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.7797 C=0.2203
ALFA Total Global 3628 T=0.7911 C=0.2089
ALFA European Sub 3292 T=0.7974 C=0.2026
ALFA African Sub 160 T=0.675 C=0.325
ALFA Other Sub 146 T=0.774 C=0.226
ALFA Latin American 2 Sub 12 T=0.67 C=0.33
ALFA Asian Sub 12 T=1.00 C=0.00
ALFA South Asian Sub 4 T=1.0 C=0.0
ALFA Latin American 1 Sub 2 T=0.0 C=1.0
KOREAN population from KRGDB KOREAN Study-wide 2922 T=0.9962 C=0.0038
Korean Genome Project KOREAN Study-wide 1832 T=0.9951 C=0.0049
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 T=0.785 C=0.215
Northern Sweden ACPOP Study-wide 600 T=0.807 C=0.193
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 T=0.788 C=0.212
Qatari Global Study-wide 216 T=0.852 C=0.148
A Vietnamese Genetic Variation Database Global Study-wide 210 T=0.967 C=0.033
SGDP_PRJ Global Study-wide 174 T=0.454 C=0.546
The Danish reference pan genome Danish Study-wide 40 T=0.72 C=0.28
Siberian Global Study-wide 10 T=0.5 C=0.5
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
GRCh38.p12 chr 3 NC_000003.12:g.120675674= NC_000003.12:g.120675674T>C
GRCh37.p13 chr 3 NC_000003.11:g.120394521= NC_000003.11:g.120394521T>C
HGD RefSeqGene NG_011957.1:g.11808= NG_011957.1:g.11808A>G
HGD transcript NM_000187.3:c.87+118= NM_000187.3:c.87+118A>G
HGD transcript NM_000187.4:c.87+118= NM_000187.4:c.87+118A>G
HGD transcript variant X1 XM_005247412.1:c.87+118= XM_005247412.1:c.87+118A>G
HGD transcript variant X1 XM_005247412.2:c.87+118= XM_005247412.2:c.87+118A>G
HGD transcript variant X2 XM_005247413.1:c.87+118= XM_005247413.1:c.87+118A>G
HGD transcript variant X2 XM_005247413.2:c.87+118= XM_005247413.2:c.87+118A>G
HGD transcript variant X3 XM_005247414.1:c.87+118= XM_005247414.1:c.87+118A>G
HGD transcript variant X5 XM_005247414.5:c.87+118= XM_005247414.5:c.87+118A>G
HGD transcript variant X4 XM_011512746.2:c.87+118= XM_011512746.2:c.87+118A>G
HGD transcript variant X3 XM_017006277.2:c.-337+118= XM_017006277.2:c.-337+118A>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#.

53 SubSNP, 17 Frequency submissions
No Submitter Submission ID Date (Build)
1 PERLEGEN ss23259088 Sep 20, 2004 (123)
2 PERLEGEN ss68873520 May 17, 2007 (127)
3 BCMHGSC_JDW ss92257458 Mar 23, 2008 (130)
4 BUSHMAN ss203091636 Jul 04, 2010 (132)
5 BL ss253439456 May 09, 2011 (134)
6 GMI ss284734978 Apr 25, 2013 (138)
7 PJP ss292899034 May 09, 2011 (134)
8 1000GENOMES ss331005043 May 09, 2011 (134)
9 ILLUMINA ss483619124 May 04, 2012 (137)
10 ILLUMINA ss484445034 May 04, 2012 (137)
11 ILLUMINA ss535823279 Sep 08, 2015 (146)
12 TISHKOFF ss556900275 Apr 25, 2013 (138)
13 SSMP ss650612162 Apr 25, 2013 (138)
14 ILLUMINA ss780345484 Aug 21, 2014 (142)
15 ILLUMINA ss782252913 Aug 21, 2014 (142)
16 ILLUMINA ss835833106 Aug 21, 2014 (142)
17 EVA-GONL ss979083999 Aug 21, 2014 (142)
18 JMKIDD_LAB ss1070777437 Aug 21, 2014 (142)
19 1000GENOMES ss1305860338 Aug 21, 2014 (142)
20 DDI ss1429564139 Apr 01, 2015 (144)
21 EVA_GENOME_DK ss1580152606 Apr 01, 2015 (144)
22 EVA_DECODE ss1588566212 Apr 01, 2015 (144)
23 EVA_UK10K_ALSPAC ss1608059812 Apr 01, 2015 (144)
24 EVA_UK10K_TWINSUK ss1651053845 Apr 01, 2015 (144)
25 EVA_MGP ss1711029912 Apr 01, 2015 (144)
26 HAMMER_LAB ss1799930932 Sep 08, 2015 (146)
27 WEILL_CORNELL_DGM ss1922310316 Feb 12, 2016 (147)
28 GENOMED ss1969505838 Jul 19, 2016 (147)
29 JJLAB ss2021723000 Sep 14, 2016 (149)
30 USC_VALOUEV ss2149815134 Dec 20, 2016 (150)
31 HUMAN_LONGEVITY ss2255255117 Dec 20, 2016 (150)
32 TOPMED ss2422579508 Dec 20, 2016 (150)
33 ILLUMINA ss2634003264 Nov 08, 2017 (151)
34 GNOMAD ss2798282203 Nov 08, 2017 (151)
35 SWEGEN ss2993074688 Nov 08, 2017 (151)
36 BIOINF_KMB_FNS_UNIBA ss3024628340 Nov 08, 2017 (151)
37 CSHL ss3345231518 Nov 08, 2017 (151)
38 TOPMED ss3403603744 Nov 08, 2017 (151)
39 ILLUMINA ss3628759206 Oct 12, 2018 (152)
40 ILLUMINA ss3631946592 Oct 12, 2018 (152)
41 ILLUMINA ss3642277982 Oct 12, 2018 (152)
42 OMUKHERJEE_ADBS ss3646291555 Oct 12, 2018 (152)
43 EGCUT_WGS ss3661001472 Jul 13, 2019 (153)
44 EVA_DECODE ss3710145808 Jul 13, 2019 (153)
45 ACPOP ss3730286897 Jul 13, 2019 (153)
46 EVA ss3760599581 Jul 13, 2019 (153)
47 KHV_HUMAN_GENOMES ss3803735868 Jul 13, 2019 (153)
48 EVA ss3828038446 Apr 25, 2020 (154)
49 EVA ss3837451420 Apr 25, 2020 (154)
50 EVA ss3842881692 Apr 25, 2020 (154)
51 SGDP_PRJ ss3856814321 Apr 25, 2020 (154)
52 KRGDB ss3902806912 Apr 25, 2020 (154)
53 KOGIC ss3952261262 Apr 25, 2020 (154)
54 1000Genomes NC_000003.11 - 120394521 Oct 12, 2018 (152)
55 The Avon Longitudinal Study of Parents and Children NC_000003.11 - 120394521 Oct 12, 2018 (152)
56 Genetic variation in the Estonian population NC_000003.11 - 120394521 Oct 12, 2018 (152)
57 The Danish reference pan genome NC_000003.11 - 120394521 Apr 25, 2020 (154)
58 gnomAD - Genomes NC_000003.11 - 120394521 Jul 13, 2019 (153)
59 Genome of the Netherlands Release 5 NC_000003.11 - 120394521 Apr 25, 2020 (154)
60 KOREAN population from KRGDB NC_000003.11 - 120394521 Apr 25, 2020 (154)
61 Korean Genome Project NC_000003.12 - 120675674 Apr 25, 2020 (154)
62 Medical Genome Project healthy controls from Spanish population NC_000003.11 - 120394521 Apr 25, 2020 (154)
63 Northern Sweden NC_000003.11 - 120394521 Jul 13, 2019 (153)
64 Qatari NC_000003.11 - 120394521 Apr 25, 2020 (154)
65 SGDP_PRJ NC_000003.11 - 120394521 Apr 25, 2020 (154)
66 Siberian NC_000003.11 - 120394521 Apr 25, 2020 (154)
67 TopMed NC_000003.12 - 120675674 Oct 12, 2018 (152)
68 UK 10K study - Twins NC_000003.11 - 120394521 Oct 12, 2018 (152)
69 A Vietnamese Genetic Variation Database NC_000003.11 - 120394521 Jul 13, 2019 (153)
70 dbGaP Population Frequency Project NC_000003.12 - 120675674 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).

Associated ID History Updated (Build)
rs61795593 May 26, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss92257458, ss203091636, ss253439456, ss284734978, ss292899034, ss484445034, ss1588566212 NC_000003.10:121877210:T:C NC_000003.12:120675673:T:C (self)
17113037, 9532748, 6739720, 6317545, 46817754, 4188026, 9984306, 145740, 3571762, 4352246, 8831301, 2331488, 9532748, 2078049, ss331005043, ss483619124, ss535823279, ss556900275, ss650612162, ss780345484, ss782252913, ss835833106, ss979083999, ss1070777437, ss1305860338, ss1429564139, ss1580152606, ss1608059812, ss1651053845, ss1711029912, ss1799930932, ss1922310316, ss1969505838, ss2021723000, ss2149815134, ss2422579508, ss2634003264, ss2798282203, ss2993074688, ss3345231518, ss3628759206, ss3631946592, ss3642277982, ss3646291555, ss3661001472, ss3730286897, ss3760599581, ss3828038446, ss3837451420, ss3856814321, ss3902806912 NC_000003.11:120394520:T:C NC_000003.12:120675673:T:C (self)
8639263, 261525003, 225215268, ss2255255117, ss3024628340, ss3403603744, ss3710145808, ss3803735868, ss3842881692, ss3952261262 NC_000003.12:120675673:T:C NC_000003.12:120675673:T:C (self)
ss23259088, ss68873520 NT_005612.16:26889666:T:C NC_000003.12:120675673: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 rs17140396

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