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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.

rs3759245

Current Build 152

Released October 2, 2018

Organism
Homo sapiens
Position
chr12:11091518 (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
A>C / A>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.05373 (6048/112556, ExAC)
G=0.1060 (2484/23434, GnomAD)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
TAS2R43 : Missense Variant
PRH1 : Intron Variant
PRH1-PRR4 : Intron Variant (+ 1 more)
PRH1-TAS2R14 : Intron Variant
Publications
1 citation
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 12 NC_000012.12:g.11091518A>C
GRCh38.p12 chr 12 NC_000012.12:g.11091518A>G
GRCh37.p13 chr 12 NC_000012.11:g.11244117A>C
GRCh37.p13 chr 12 NC_000012.11:g.11244117A>G
GRCh38.p12 chr 12 alt locus HSCHR12_3_CTG2 NT_187658.1:g.292075G>A
GRCh38.p12 chr 12 alt locus HSCHR12_3_CTG2 NT_187658.1:g.292075G>C
GRCh37.p13 chr 12 novel patch HG1133_PATCH NW_003571047.1:g.292087G>A
GRCh37.p13 chr 12 novel patch HG1133_PATCH NW_003571047.1:g.292087G>C
GRCh38.p12 chr 12 alt locus HSCHR12_2_CTG2 NW_003571050.1:g.290245A>C
GRCh38.p12 chr 12 alt locus HSCHR12_2_CTG2 NW_003571050.1:g.290245A>G
Gene: PRH1, proline rich protein HaeIII subfamily 1 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
PRH1 transcript variant 1 NM_001291314.1:c. N/A Intron Variant
PRH1 transcript variant 2 NM_001291315.1:c. N/A Intron Variant
PRH1 transcript variant 3 NR_133575.1:n. N/A Intron Variant
Gene: PRH1-TAS2R14, PRH1-TAS2R14 readthrough (minus strand)
Molecule type Change Amino acid[Codon] SO Term
PRH1-TAS2R14 transcript NM_001316893.1:c. N/A Intron Variant
Gene: TAS2R43, taste 2 receptor member 43 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
TAS2R43 transcript NM_176884.2:c.712T>G C [TGT] > G [GGT] Coding Sequence Variant
taste receptor type 2 member 43 NP_795365.2:p.Cys238Gly C (Cys) > G (Gly) Missense Variant
TAS2R43 transcript NM_176884.2:c.712T>C C [TGT] > R [CGT] Coding Sequence Variant
taste receptor type 2 member 43 NP_795365.2:p.Cys238Arg C (Cys) > R (Arg) Missense Variant
Gene: PRH1-PRR4, PRH1-PRR4 readthrough (minus strand)
Molecule type Change Amino acid[Codon] SO Term
PRH1-PRR4 transcript NR_037918.2:n. 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
ExAC Global Study-wide 112556 A=0.94627 G=0.05373
ExAC Europe Sub 67158 A=0.9310 G=0.0690
ExAC Asian Sub 24038 A=0.9841 G=0.0159
ExAC American Sub 10902 A=0.9408 G=0.0592
ExAC African Sub 9636 A=0.963 G=0.037
ExAC Other Sub 822 A=0.96 G=0.04
gnomAD - Genomes Global Study-wide 23434 A=0.8940 G=0.1060
gnomAD - Genomes European Sub 13530 A=0.8871 G=0.1129
gnomAD - Genomes African Sub 6928 A=0.910 G=0.090
gnomAD - Genomes East Asian Sub 1320 A=0.890 G=0.110
gnomAD - Genomes Other Sub 726 A=0.87 G=0.13
gnomAD - Genomes American Sub 676 A=0.87 G=0.13
gnomAD - Genomes Ashkenazi Jewish Sub 254 A=0.99 G=0.01
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 A= C G Note
GRCh38.p12 chr 12 NC_000012.12:g.11...

NC_000012.12:g.11091518A=

NC_000012.12:g.11...

NC_000012.12:g.11091518A>C

NC_000012.12:g.11...

NC_000012.12:g.11091518A>G

GRCh37.p13 chr 12 NC_000012.11:g.11...

NC_000012.11:g.11244117A=

NC_000012.11:g.11...

NC_000012.11:g.11244117A>C

NC_000012.11:g.11...

NC_000012.11:g.11244117A>G

GRCh38.p12 chr 12 alt locus HSCHR12_3_CTG2 NT_187658.1:g.292...

NT_187658.1:g.292075G>A

NT_187658.1:g.292...

NT_187658.1:g.292075G>C

NT_187658.1:g.292...

NT_187658.1:g.292075G=

GRCh37.p13 chr 12 novel patch HG1133_PATCH NW_003571047.1:g....

NW_003571047.1:g.292087G>A

NW_003571047.1:g....

NW_003571047.1:g.292087G>C

NW_003571047.1:g....

NW_003571047.1:g.292087G=

GRCh38.p12 chr 12 alt locus HSCHR12_2_CTG2 NW_003571050.1:g....

NW_003571050.1:g.290245A=

NW_003571050.1:g....

NW_003571050.1:g.290245A>C

NW_003571050.1:g....

NW_003571050.1:g.290245A>G

TAS2R43 transcript variant X1 XM_003960991.5:c....

XM_003960991.5:c.712C>T

XM_003960991.5:c....

XM_003960991.5:c.712C>G

XM_003960991.5:c....

XM_003960991.5:c.712C=

TAS2R43 transcript XM_003960991.2:c....

XM_003960991.2:c.712C>T

XM_003960991.2:c....

XM_003960991.2:c.712C>G

XM_003960991.2:c....

XM_003960991.2:c.712C=

TAS2R43 transcript NM_176884.2:c.712T= NM_176884.2:c.712T>G NM_176884.2:c.712T>C
taste receptor type 2 member 43 NP_795365.2:p.Cys...

NP_795365.2:p.Cys238=

NP_795365.2:p.Cys...

NP_795365.2:p.Cys238Gly

NP_795365.2:p.Cys...

NP_795365.2:p.Cys238Arg

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#.

25 SubSNP, 2 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_SNP ss15973493 Feb 27, 2004 (120)
2 ILLUMINA ss482975441 May 04, 2012 (142)
3 ILLUMINA ss483699080 May 04, 2012 (142)
4 EXOME_CHIP ss491464458 May 04, 2012 (142)
5 CLINSEQ_SNP ss491660712 May 04, 2012 (142)
6 ILLUMINA ss535900726 Sep 08, 2015 (146)
7 SSMP ss658524719 Apr 25, 2013 (142)
8 ILLUMINA ss780375374 Aug 21, 2014 (142)
9 ILLUMINA ss782293038 Aug 21, 2014 (142)
10 ILLUMINA ss835863625 Aug 21, 2014 (142)
11 EVA_EXAC ss1690796289 Apr 01, 2015 (144)
12 EVA_MGP ss1711321373 Apr 01, 2015 (144)
13 USC_VALOUEV ss2155370649 Dec 20, 2016 (150)
14 ILLUMINA ss2632924989 Nov 08, 2017 (151)
15 GNOMAD ss2739640621 Nov 08, 2017 (151)
16 GNOMAD ss2748815861 Nov 08, 2017 (151)
17 GNOMAD ss2907343307 Nov 08, 2017 (151)
18 AFFY ss2984968049 Nov 08, 2017 (151)
19 SWEGEN ss3009208584 Nov 08, 2017 (151)
20 TOPMED ss3162953094 Nov 08, 2017 (151)
21 ILLUMINA ss3626816463 Oct 12, 2018 (152)
22 ILLUMINA ss3630936698 Oct 12, 2018 (152)
23 ILLUMINA ss3641775301 Oct 12, 2018 (152)
24 OMUKHERJEE_ADBS ss3646438399 Oct 12, 2018 (152)
25 ILLUMINA ss3653740390 Oct 12, 2018 (152)
26 ExAC NC_000012.11 - 11244117 Oct 12, 2018 (152)
27 gnomAD - Genomes NC_000012.11 - 11244117 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).

Associated ID History Updated (Build)
rs201758916 Aug 21, 2014 (142)
Added to this RefSNP Cluster:
Submission ids Observation SPDI Canonical SPDI Source RSIDs
ss482975441, ss491660712 NC_000012.10:11135383:A= NC_000012.12:11091517:A= (self)
1084226, 41044830, ss483699080, ss491464458, ss535900726, ss658524719, ss780375374, ss782293038, ss835863625, ss1690796289, ss1711321373, ss2155370649, ss2632924989, ss2739640621, ss2748815861, ss2907343307, ss2984968049, ss3009208584, ss3626816463, ss3630936698, ss3641775301, ss3646438399, ss3653740390 NC_000012.11:11244116:A= NC_000012.12:11091517:A= (self)
ss3162953094 NC_000012.12:11091517:A= NC_000012.12:11091517:A= (self)
ss15973493 NT_079586.1:412094:T= NC_000012.12:11091517:A= (self)
ss3646438399 NC_000012.11:11244116:A>C NC_000012.12:11091517:A>C
ss482975441, ss491660712 NC_000012.10:11135383:A>G NC_000012.12:11091517:A>G (self)
1084226, 41044830, ss483699080, ss491464458, ss535900726, ss658524719, ss780375374, ss782293038, ss835863625, ss1690796289, ss1711321373, ss2155370649, ss2632924989, ss2739640621, ss2748815861, ss2907343307, ss2984968049, ss3009208584, ss3626816463, ss3630936698, ss3641775301, ss3653740390 NC_000012.11:11244116:A>G NC_000012.12:11091517:A>G (self)
ss3162953094 NC_000012.12:11091517:A>G NC_000012.12:11091517:A>G (self)
ss15973493 NT_079586.1:412094:T>C NC_000012.12:11091517:A>G (self)
Help

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

1 citation for rs3759245
PMID Title Author Year Journal
19092995 Bitter taste receptors influence glucose homeostasis. Dotson CD et al. 2008 PloS one

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.post58+e54ea20