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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.

rs1466745839

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr9:70811515 (GRCh38.p14) 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>A
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.000007 (1/140216, GnomAD)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
TRPM3 : Intron Variant
MIR204 : 2KB Upstream Variant
Publications
0 citations
Genomic View
See rs on genome
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 - Genomes Global Study-wide 140216 G=0.999993 A=0.000007
gnomAD - Genomes European Sub 75932 G=0.99999 A=0.00001
gnomAD - Genomes African Sub 42030 G=1.00000 A=0.00000
gnomAD - Genomes American Sub 13650 G=1.00000 A=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3322 G=1.0000 A=0.0000
gnomAD - Genomes East Asian Sub 3130 G=1.0000 A=0.0000
gnomAD - Genomes Other Sub 2152 G=1.0000 A=0.0000
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.p14 chr 9 NC_000009.12:g.70811515G>A
GRCh37.p13 chr 9 NC_000009.11:g.73426431G>A
TRPM3 RefSeqGene NG_047197.1:g.640410C>T
Gene: TRPM3, transient receptor potential cation channel subfamily M member 3 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
TRPM3 transcript variant 8 NM_001007470.3:c.515-271C…

NM_001007470.3:c.515-271C>T

N/A Intron Variant
TRPM3 transcript variant 9 NM_001007471.4:c.973+1633…

NM_001007471.4:c.973+16332C>T

N/A Intron Variant
TRPM3 transcript variant 10 NM_001366141.2:c.979+1633…

NM_001366141.2:c.979+16332C>T

N/A Intron Variant
TRPM3 transcript variant 11 NM_001366142.2:c.979+1633…

NM_001366142.2:c.979+16332C>T

N/A Intron Variant
TRPM3 transcript variant 12 NM_001366143.2:c.979+1633…

NM_001366143.2:c.979+16332C>T

N/A Intron Variant
TRPM3 transcript variant 13 NM_001366144.2:c.979+1633…

NM_001366144.2:c.979+16332C>T

N/A Intron Variant
TRPM3 transcript variant 14 NM_001366145.2:c.973+1633…

NM_001366145.2:c.973+16332C>T

N/A Intron Variant
TRPM3 transcript variant 15 NM_001366146.2:c.973+1633…

NM_001366146.2:c.973+16332C>T

N/A Intron Variant
TRPM3 transcript variant 16 NM_001366147.2:c.974-271C…

NM_001366147.2:c.974-271C>T

N/A Intron Variant
TRPM3 transcript variant 17 NM_001366148.2:c.974-271C…

NM_001366148.2:c.974-271C>T

N/A Intron Variant
TRPM3 transcript variant 18 NM_001366149.2:c.973+1633…

NM_001366149.2:c.973+16332C>T

N/A Intron Variant
TRPM3 transcript variant 19 NM_001366150.2:c.973+1633…

NM_001366150.2:c.973+16332C>T

N/A Intron Variant
TRPM3 transcript variant 20 NM_001366151.2:c.973+1633…

NM_001366151.2:c.973+16332C>T

N/A Intron Variant
TRPM3 transcript variant 21 NM_001366152.2:c.974-271C…

NM_001366152.2:c.974-271C>T

N/A Intron Variant
TRPM3 transcript variant 22 NM_001366153.2:c.973+1633…

NM_001366153.2:c.973+16332C>T

N/A Intron Variant
TRPM3 transcript variant 23 NM_001366154.2:c.514+1633…

NM_001366154.2:c.514+16332C>T

N/A Intron Variant
TRPM3 transcript variant 1 NM_020952.6:c.514+16332C>T N/A Intron Variant
TRPM3 transcript variant 2 NM_024971.7:c.514+16332C>T N/A Intron Variant
TRPM3 transcript variant 3 NM_206944.5:c.514+16332C>T N/A Intron Variant
TRPM3 transcript variant 4 NM_206945.5:c.514+16332C>T N/A Intron Variant
TRPM3 transcript variant 5 NM_206946.5:c.515-271C>T N/A Intron Variant
TRPM3 transcript variant 6 NM_206947.5:c.515-271C>T N/A Intron Variant
TRPM3 transcript variant 7 NM_206948.4:c.514+16332C>T N/A Intron Variant
Gene: MIR204, microRNA 204 (minus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
MIR204 transcript NR_029621.1:n. N/A Upstream 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

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= A
GRCh38.p14 chr 9 NC_000009.12:g.70811515= NC_000009.12:g.70811515G>A
GRCh37.p13 chr 9 NC_000009.11:g.73426431= NC_000009.11:g.73426431G>A
TRPM3 RefSeqGene NG_047197.1:g.640410= NG_047197.1:g.640410C>T
TRPM3 transcript variant 8 NM_001007470.1:c.515-271= NM_001007470.1:c.515-271C>T
TRPM3 transcript variant 8 NM_001007470.3:c.515-271= NM_001007470.3:c.515-271C>T
TRPM3 transcript variant 9 NM_001007471.2:c.973+16332= NM_001007471.2:c.973+16332C>T
TRPM3 transcript variant 9 NM_001007471.4:c.973+16332= NM_001007471.4:c.973+16332C>T
TRPM3 transcript variant 10 NM_001366141.2:c.979+16332= NM_001366141.2:c.979+16332C>T
TRPM3 transcript variant 11 NM_001366142.2:c.979+16332= NM_001366142.2:c.979+16332C>T
TRPM3 transcript variant 12 NM_001366143.2:c.979+16332= NM_001366143.2:c.979+16332C>T
TRPM3 transcript variant 13 NM_001366144.2:c.979+16332= NM_001366144.2:c.979+16332C>T
TRPM3 transcript variant 14 NM_001366145.2:c.973+16332= NM_001366145.2:c.973+16332C>T
TRPM3 transcript variant 15 NM_001366146.2:c.973+16332= NM_001366146.2:c.973+16332C>T
TRPM3 transcript variant 16 NM_001366147.2:c.974-271= NM_001366147.2:c.974-271C>T
TRPM3 transcript variant 17 NM_001366148.2:c.974-271= NM_001366148.2:c.974-271C>T
TRPM3 transcript variant 18 NM_001366149.2:c.973+16332= NM_001366149.2:c.973+16332C>T
TRPM3 transcript variant 19 NM_001366150.2:c.973+16332= NM_001366150.2:c.973+16332C>T
TRPM3 transcript variant 20 NM_001366151.2:c.973+16332= NM_001366151.2:c.973+16332C>T
TRPM3 transcript variant 21 NM_001366152.2:c.974-271= NM_001366152.2:c.974-271C>T
TRPM3 transcript variant 22 NM_001366153.2:c.973+16332= NM_001366153.2:c.973+16332C>T
TRPM3 transcript variant 23 NM_001366154.2:c.514+16332= NM_001366154.2:c.514+16332C>T
TRPM3 transcript variant 1 NM_020952.4:c.514+16332= NM_020952.4:c.514+16332C>T
TRPM3 transcript variant 1 NM_020952.6:c.514+16332= NM_020952.6:c.514+16332C>T
TRPM3 transcript variant 2 NM_024971.5:c.514+16332= NM_024971.5:c.514+16332C>T
TRPM3 transcript variant 2 NM_024971.7:c.514+16332= NM_024971.7:c.514+16332C>T
TRPM3 transcript variant 3 NM_206944.3:c.514+16332= NM_206944.3:c.514+16332C>T
TRPM3 transcript variant 3 NM_206944.5:c.514+16332= NM_206944.5:c.514+16332C>T
TRPM3 transcript variant 4 NM_206945.3:c.514+16332= NM_206945.3:c.514+16332C>T
TRPM3 transcript variant 4 NM_206945.5:c.514+16332= NM_206945.5:c.514+16332C>T
TRPM3 transcript variant 5 NM_206946.3:c.515-271= NM_206946.3:c.515-271C>T
TRPM3 transcript variant 5 NM_206946.5:c.515-271= NM_206946.5:c.515-271C>T
TRPM3 transcript variant 6 NM_206947.3:c.515-271= NM_206947.3:c.515-271C>T
TRPM3 transcript variant 6 NM_206947.5:c.515-271= NM_206947.5:c.515-271C>T
TRPM3 transcript variant 7 NM_206948.2:c.514+16332= NM_206948.2:c.514+16332C>T
TRPM3 transcript variant 7 NM_206948.4:c.514+16332= NM_206948.4:c.514+16332C>T
TRPM3 transcript variant X1 XM_005252217.1:c.974-271= XM_005252217.1:c.974-271C>T
TRPM3 transcript variant X2 XM_005252218.1:c.980-271= XM_005252218.1:c.980-271C>T
TRPM3 transcript variant X3 XM_005252219.1:c.974-271= XM_005252219.1:c.974-271C>T
TRPM3 transcript variant X4 XM_005252220.1:c.974-271= XM_005252220.1:c.974-271C>T
TRPM3 transcript variant X5 XM_005252221.1:c.973+16332= XM_005252221.1:c.973+16332C>T
TRPM3 transcript variant X6 XM_005252222.1:c.974-271= XM_005252222.1:c.974-271C>T
TRPM3 transcript variant X7 XM_005252223.1:c.979+16332= XM_005252223.1:c.979+16332C>T
TRPM3 transcript variant X8 XM_005252224.1:c.979+16332= XM_005252224.1:c.979+16332C>T
TRPM3 transcript variant X9 XM_005252225.1:c.973+16332= XM_005252225.1:c.973+16332C>T
TRPM3 transcript variant X10 XM_005252226.1:c.973+16332= XM_005252226.1:c.973+16332C>T
TRPM3 transcript variant X11 XM_005252227.1:c.974-271= XM_005252227.1:c.974-271C>T
TRPM3 transcript variant X12 XM_005252228.1:c.979+16332= XM_005252228.1:c.979+16332C>T
TRPM3 transcript variant X13 XM_005252229.1:c.979+16332= XM_005252229.1:c.979+16332C>T
TRPM3 transcript variant X14 XM_005252230.1:c.973+16332= XM_005252230.1:c.973+16332C>T
TRPM3 transcript variant X15 XM_005252231.1:c.973+16332= XM_005252231.1:c.973+16332C>T
TRPM3 transcript variant X16 XM_005252232.1:c.979+16332= XM_005252232.1:c.979+16332C>T
TRPM3 transcript variant X17 XM_005252233.1:c.973+16332= XM_005252233.1:c.973+16332C>T
TRPM3 transcript variant X18 XM_005252234.1:c.973+16332= XM_005252234.1:c.973+16332C>T
TRPM3 transcript variant X19 XM_005252235.1:c.973+16332= XM_005252235.1:c.973+16332C>T
TRPM3 transcript variant X20 XM_005252236.1:c.973+16332= XM_005252236.1:c.973+16332C>T
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#.

1 SubSNP, 1 Frequency submissions
No Submitter Submission ID Date (Build)
1 GNOMAD ss2878983346 Nov 08, 2017 (151)
2 gnomAD - Genomes NC_000009.12 - 70811515 Apr 27, 2021 (155)
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
ss2878983346 NC_000009.11:73426430:G:A NC_000009.12:70811514:G:A (self)
326860798 NC_000009.12:70811514:G:A NC_000009.12:70811514:G:A (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 rs1466745839

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.post820+afb47a3d