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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.

rs17140398

Current Build 153

Released July 9, 2019

Organism
Homo sapiens
Position
chr3:120676038 (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
G>C / G>T
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.43572 (54713/125568, TOPMED)
C=0.409 (2048/5008, 1000G)
C=0.369 (1651/4480, Estonian) (+ 4 more)
C=0.369 (1422/3854, ALSPAC)
C=0.379 (1404/3708, TWINSUK)
C=0.41 (244/600, NorthernSweden)
C=0.20 (43/214, 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.120676038G>C
GRCh38.p12 chr 3 NC_000003.12:g.120676038G>T
GRCh37.p13 chr 3 NC_000003.11:g.120394885G>C
GRCh37.p13 chr 3 NC_000003.11:g.120394885G>T
HGD RefSeqGene NG_011957.1:g.11444C>G
HGD RefSeqGene NG_011957.1:g.11444C>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 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
TopMed Global Study-wide 125568 G=0.56428 C=0.43572
1000Genomes Global Study-wide 5008 G=0.591 C=0.409
1000Genomes African Sub 1322 G=0.326 C=0.674
1000Genomes East Asian Sub 1008 G=0.809 C=0.191
1000Genomes Europe Sub 1006 G=0.606 C=0.394
1000Genomes South Asian Sub 978 G=0.71 C=0.29
1000Genomes American Sub 694 G=0.59 C=0.41
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.631 C=0.369
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.631 C=0.369
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.621 C=0.379
Northern Sweden ACPOP Study-wide 600 G=0.59 C=0.41
A Vietnamese Genetic Variation Database Global Study-wide 214 G=0.80 C=0.20
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 G= C T Note
GRCh38.p12 chr 3 NC_000003.12:g.12...

NC_000003.12:g.120676038=

NC_000003.12:g.12...

NC_000003.12:g.120676038G>C

NC_000003.12:g.12...

NC_000003.12:g.120676038G>T

GRCh37.p13 chr 3 NC_000003.11:g.12...

NC_000003.11:g.120394885=

NC_000003.11:g.12...

NC_000003.11:g.120394885G>C

NC_000003.11:g.12...

NC_000003.11:g.120394885G>T

HGD RefSeqGene NG_011957.1:g.11444= NG_011957.1:g.114...

NG_011957.1:g.11444C>G

NG_011957.1:g.114...

NG_011957.1:g.11444C>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#.

47 SubSNP, 9 Frequency submissions
No Submitter Submission ID Date (Build)
1 PERLEGEN ss23259109 Sep 20, 2004 (123)
2 BCMHGSC_JDW ss92257460 Mar 23, 2008 (130)
3 BGI ss103978176 Dec 01, 2009 (131)
4 GMI ss156111594 Dec 01, 2009 (131)
5 COMPLETE_GENOMICS ss162547920 Jul 04, 2010 (132)
6 COMPLETE_GENOMICS ss164111074 Jul 04, 2010 (132)
7 COMPLETE_GENOMICS ss167113224 Jul 04, 2010 (132)
8 BUSHMAN ss203091640 Jul 04, 2010 (132)
9 BCM-HGSC-SUB ss206050463 Jul 04, 2010 (132)
10 BL ss253439461 May 09, 2011 (134)
11 GMI ss277320446 May 04, 2012 (137)
12 GMI ss284734979 Apr 25, 2013 (138)
13 PJP ss292899035 May 09, 2011 (134)
14 1000GENOMES ss331005045 May 09, 2011 (134)
15 TISHKOFF ss556900277 Apr 25, 2013 (138)
16 SSMP ss650612165 Apr 25, 2013 (138)
17 EVA-GONL ss979084002 Aug 21, 2014 (142)
18 JMKIDD_LAB ss1070777439 Aug 21, 2014 (142)
19 1000GENOMES ss1305860347 Aug 21, 2014 (142)
20 DDI ss1429564141 Apr 01, 2015 (144)
21 EVA_GENOME_DK ss1580152608 Apr 01, 2015 (144)
22 EVA_DECODE ss1588566214 Apr 01, 2015 (144)
23 EVA_UK10K_ALSPAC ss1608059815 Apr 01, 2015 (144)
24 EVA_UK10K_TWINSUK ss1651053848 Apr 01, 2015 (144)
25 EVA_MGP ss1711029914 Apr 01, 2015 (144)
26 HAMMER_LAB ss1799930935 Sep 08, 2015 (146)
27 WEILL_CORNELL_DGM ss1922310318 Feb 12, 2016 (147)
28 GENOMED ss1969505839 Jul 19, 2016 (147)
29 JJLAB ss2021723002 Sep 14, 2016 (149)
30 USC_VALOUEV ss2149815136 Dec 20, 2016 (150)
31 HUMAN_LONGEVITY ss2255255136 Dec 20, 2016 (150)
32 TOPMED ss2422579527 Dec 20, 2016 (150)
33 SYSTEMSBIOZJU ss2625363342 Nov 08, 2017 (151)
34 GRF ss2705218426 Nov 08, 2017 (151)
35 GNOMAD ss2798282232 Nov 08, 2017 (151)
36 BIOINF_KMB_FNS_UNIBA ss3024628342 Nov 08, 2017 (151)
37 CSHL ss3345231520 Nov 08, 2017 (151)
38 TOPMED ss3403603797 Nov 08, 2017 (151)
39 TOPMED ss3403603798 Nov 08, 2017 (151)
40 EGCUT_WGS ss3661001478 Jul 13, 2019 (153)
41 EVA_DECODE ss3710145811 Jul 13, 2019 (153)
42 ACPOP ss3730286899 Jul 13, 2019 (153)
43 EVA ss3760599586 Jul 13, 2019 (153)
44 PACBIO ss3784443354 Jul 13, 2019 (153)
45 PACBIO ss3789940802 Jul 13, 2019 (153)
46 PACBIO ss3794815237 Jul 13, 2019 (153)
47 KHV_HUMAN_GENOMES ss3803735871 Jul 13, 2019 (153)
48 1000Genomes NC_000003.11 - 120394885 Oct 12, 2018 (152)
49 The Avon Longitudinal Study of Parents and Children NC_000003.11 - 120394885 Oct 12, 2018 (152)
50 Genetic variation in the Estonian population NC_000003.11 - 120394885 Oct 12, 2018 (152)
51 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 46817782 (NC_000003.11:120394884:G:G 17912/31320, NC_000003.11:120394884:G:C 13408/31320)
Row 46817783 (NC_000003.11:120394884:G:G 31318/31320, NC_000003.11:120394884:G:T 2/31320)

- Jul 13, 2019 (153)
52 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 46817782 (NC_000003.11:120394884:G:G 17912/31320, NC_000003.11:120394884:G:C 13408/31320)
Row 46817783 (NC_000003.11:120394884:G:G 31318/31320, NC_000003.11:120394884:G:T 2/31320)

- Jul 13, 2019 (153)
53 Northern Sweden NC_000003.11 - 120394885 Jul 13, 2019 (153)
54 TopMed NC_000003.12 - 120676038 Oct 12, 2018 (152)
55 UK 10K study - Twins NC_000003.11 - 120394885 Oct 12, 2018 (152)
56 A Vietnamese Genetic Variation Database NC_000003.11 - 120394885 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)
rs61795594 May 25, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss92257460, ss162547920, ss164111074, ss167113224, ss203091640, ss206050463, ss253439461, ss277320446, ss284734979, ss292899035, ss1588566214 NC_000003.10:121877574:G:C NC_000003.12:120676037:G:C (self)
17113046, 9532751, 6739726, 3571764, 9532751, 2078051, ss331005045, ss556900277, ss650612165, ss979084002, ss1070777439, ss1305860347, ss1429564141, ss1580152608, ss1608059815, ss1651053848, ss1711029914, ss1799930935, ss1922310318, ss1969505839, ss2021723002, ss2149815136, ss2422579527, ss2625363342, ss2705218426, ss2798282232, ss3345231520, ss3661001478, ss3730286899, ss3760599586, ss3784443354, ss3789940802, ss3794815237 NC_000003.11:120394884:G:C NC_000003.12:120676037:G:C (self)
261525054, ss2255255136, ss3024628342, ss3403603797, ss3710145811, ss3803735871 NC_000003.12:120676037:G:C NC_000003.12:120676037:G:C (self)
ss23259109, ss103978176, ss156111594 NT_005612.16:26890030:G:C NC_000003.12:120676037:G:C (self)
ss2798282232 NC_000003.11:120394884:G:T NC_000003.12:120676037:G:T (self)
ss3403603798 NC_000003.12:120676037:G:T NC_000003.12:120676037:G: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 rs17140398

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