Name: rs139731407
Published: September 21, 2022
License: Open Access

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.

rs139731407

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr9:70924498 (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=0.000253 (67/264690, TOPMED)
A=0.000214 (30/140156, GnomAD)
A=0.00007 (1/14050, ALFA) (+ 5 more)
A=0.0006 (4/6404, 1000G_30x)
A=0.0008 (4/5008, 1000G)
A=0.005 (1/216, Qatari)
G=0.5 (3/6, SGDP_PRJ)
A=0.5 (3/6, SGDP_PRJ)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: TRPM3 : Intron Variant
Publications: 0 citations
Genomic View: See rs on genome

ALFA Allele Frequency
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: 20230706150541

Population	Group	Sample Size	Ref Allele	Alt Allele
Total	Global	14050	G=0.99993	A=0.00007
European	Sub	9690	G=1.0000	A=0.0000
African	Sub	2898	G=0.9997	A=0.0003
African Others	Sub	114	G=1.000	A=0.000
African American	Sub	2784	G=0.9996	A=0.0004
Asian	Sub	112	G=1.000	A=0.000
East Asian	Sub	86	G=1.00	A=0.00
Other Asian	Sub	26	G=1.00	A=0.00
Latin American 1	Sub	146	G=1.000	A=0.000
Latin American 2	Sub	610	G=1.000	A=0.000
South Asian	Sub	98	G=1.00	A=0.00
Other	Sub	496	G=1.000	A=0.000

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	264690	G=0.999747	A=0.000253
gnomAD - Genomes	Global	Study-wide	140156	G=0.999786	A=0.000214
gnomAD - Genomes	European	Sub	75916	G=1.00000	A=0.00000
gnomAD - Genomes	African	Sub	42016	G=0.99936	A=0.00064
gnomAD - Genomes	American	Sub	13620	G=0.99985	A=0.00015
gnomAD - Genomes	Ashkenazi Jewish	Sub	3322	G=1.0000	A=0.0000
gnomAD - Genomes	East Asian	Sub	3130	G=0.9997	A=0.0003
gnomAD - Genomes	Other	Sub	2152	G=1.0000	A=0.0000
Allele Frequency Aggregator	Total	Global	14050	G=0.99993	A=0.00007
Allele Frequency Aggregator	European	Sub	9690	G=1.0000	A=0.0000
Allele Frequency Aggregator	African	Sub	2898	G=0.9997	A=0.0003
Allele Frequency Aggregator	Latin American 2	Sub	610	G=1.000	A=0.000
Allele Frequency Aggregator	Other	Sub	496	G=1.000	A=0.000
Allele Frequency Aggregator	Latin American 1	Sub	146	G=1.000	A=0.000
Allele Frequency Aggregator	Asian	Sub	112	G=1.000	A=0.000
Allele Frequency Aggregator	South Asian	Sub	98	G=1.00	A=0.00
1000Genomes_30x	Global	Study-wide	6404	G=0.9994	A=0.0006
1000Genomes_30x	African	Sub	1786	G=0.9978	A=0.0022
1000Genomes_30x	Europe	Sub	1266	G=1.0000	A=0.0000
1000Genomes_30x	South Asian	Sub	1202	G=1.0000	A=0.0000
1000Genomes_30x	East Asian	Sub	1170	G=1.0000	A=0.0000
1000Genomes_30x	American	Sub	980	G=1.000	A=0.000
1000Genomes	Global	Study-wide	5008	G=0.9992	A=0.0008
1000Genomes	African	Sub	1322	G=0.9970	A=0.0030
1000Genomes	East Asian	Sub	1008	G=1.0000	A=0.0000
1000Genomes	Europe	Sub	1006	G=1.0000	A=0.0000
1000Genomes	South Asian	Sub	978	G=1.000	A=0.000
1000Genomes	American	Sub	694	G=1.000	A=0.000
Qatari	Global	Study-wide	216	G=0.995	A=0.005
SGDP_PRJ	Global	Study-wide	6	G=0.5	A=0.5

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.70924498G>A
GRCh37.p13 chr 9	NC_000009.11:g.73539414G>A
TRPM3 RefSeqGene	NG_047197.1:g.527427C>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 9	NM_001007471.4:c.178-5998… NM_001007471.4:c.178-59987C>T	N/A	Intron Variant
TRPM3 transcript variant 10	NM_001366141.2:c.184-5998… NM_001366141.2:c.184-59987C>T	N/A	Intron Variant
TRPM3 transcript variant 11	NM_001366142.2:c.184-5998… NM_001366142.2:c.184-59987C>T	N/A	Intron Variant
TRPM3 transcript variant 12	NM_001366143.2:c.184-5998… NM_001366143.2:c.184-59987C>T	N/A	Intron Variant
TRPM3 transcript variant 13	NM_001366144.2:c.184-5998… NM_001366144.2:c.184-59987C>T	N/A	Intron Variant
TRPM3 transcript variant 14	NM_001366145.2:c.178-5998… NM_001366145.2:c.178-59987C>T	N/A	Intron Variant
TRPM3 transcript variant 15	NM_001366146.2:c.178-5998… NM_001366146.2:c.178-59987C>T	N/A	Intron Variant
TRPM3 transcript variant 16	NM_001366147.2:c.178-5998… NM_001366147.2:c.178-59987C>T	N/A	Intron Variant
TRPM3 transcript variant 17	NM_001366148.2:c.178-5998… NM_001366148.2:c.178-59987C>T	N/A	Intron Variant
TRPM3 transcript variant 18	NM_001366149.2:c.178-5998… NM_001366149.2:c.178-59987C>T	N/A	Intron Variant
TRPM3 transcript variant 19	NM_001366150.2:c.178-5998… NM_001366150.2:c.178-59987C>T	N/A	Intron Variant
TRPM3 transcript variant 20	NM_001366151.2:c.178-5998… NM_001366151.2:c.178-59987C>T	N/A	Intron Variant
TRPM3 transcript variant 21	NM_001366152.2:c.178-5998… NM_001366152.2:c.178-59987C>T	N/A	Intron Variant
TRPM3 transcript variant 22	NM_001366153.2:c.178-5998… NM_001366153.2:c.178-59987C>T	N/A	Intron Variant
TRPM3 transcript variant 8	NM_001007470.3:c.	N/A	Genic Upstream Transcript Variant
TRPM3 transcript variant 23	NM_001366154.2:c.	N/A	Genic Upstream Transcript Variant
TRPM3 transcript variant 1	NM_020952.6:c.	N/A	Genic Upstream Transcript Variant
TRPM3 transcript variant 2	NM_024971.7:c.	N/A	Genic Upstream Transcript Variant
TRPM3 transcript variant 3	NM_206944.5:c.	N/A	Genic Upstream Transcript Variant
TRPM3 transcript variant 4	NM_206945.5:c.	N/A	Genic Upstream Transcript Variant
TRPM3 transcript variant 5	NM_206946.5:c.	N/A	Genic Upstream Transcript Variant
TRPM3 transcript variant 6	NM_206947.5:c.	N/A	Genic Upstream Transcript Variant
TRPM3 transcript variant 7	NM_206948.4:c.	N/A	Genic Upstream Transcript Variant

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

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.70924498=	NC_000009.12:g.70924498G>A
GRCh37.p13 chr 9	NC_000009.11:g.73539414=	NC_000009.11:g.73539414G>A
TRPM3 RefSeqGene	NG_047197.1:g.527427=	NG_047197.1:g.527427C>T
TRPM3 transcript variant 9	NM_001007471.2:c.178-59987=	NM_001007471.2:c.178-59987C>T
TRPM3 transcript variant 9	NM_001007471.4:c.178-59987=	NM_001007471.4:c.178-59987C>T
TRPM3 transcript variant 10	NM_001366141.2:c.184-59987=	NM_001366141.2:c.184-59987C>T
TRPM3 transcript variant 11	NM_001366142.2:c.184-59987=	NM_001366142.2:c.184-59987C>T
TRPM3 transcript variant 12	NM_001366143.2:c.184-59987=	NM_001366143.2:c.184-59987C>T
TRPM3 transcript variant 13	NM_001366144.2:c.184-59987=	NM_001366144.2:c.184-59987C>T
TRPM3 transcript variant 14	NM_001366145.2:c.178-59987=	NM_001366145.2:c.178-59987C>T
TRPM3 transcript variant 15	NM_001366146.2:c.178-59987=	NM_001366146.2:c.178-59987C>T
TRPM3 transcript variant 16	NM_001366147.2:c.178-59987=	NM_001366147.2:c.178-59987C>T
TRPM3 transcript variant 17	NM_001366148.2:c.178-59987=	NM_001366148.2:c.178-59987C>T
TRPM3 transcript variant 18	NM_001366149.2:c.178-59987=	NM_001366149.2:c.178-59987C>T
TRPM3 transcript variant 19	NM_001366150.2:c.178-59987=	NM_001366150.2:c.178-59987C>T
TRPM3 transcript variant 20	NM_001366151.2:c.178-59987=	NM_001366151.2:c.178-59987C>T
TRPM3 transcript variant 21	NM_001366152.2:c.178-59987=	NM_001366152.2:c.178-59987C>T
TRPM3 transcript variant 22	NM_001366153.2:c.178-59987=	NM_001366153.2:c.178-59987C>T
TRPM3 transcript variant X1	XM_005252217.1:c.178-59987=	XM_005252217.1:c.178-59987C>T
TRPM3 transcript variant X2	XM_005252218.1:c.184-59987=	XM_005252218.1:c.184-59987C>T
TRPM3 transcript variant X3	XM_005252219.1:c.178-59987=	XM_005252219.1:c.178-59987C>T
TRPM3 transcript variant X4	XM_005252220.1:c.178-59987=	XM_005252220.1:c.178-59987C>T
TRPM3 transcript variant X5	XM_005252221.1:c.178-59987=	XM_005252221.1:c.178-59987C>T
TRPM3 transcript variant X6	XM_005252222.1:c.178-59987=	XM_005252222.1:c.178-59987C>T
TRPM3 transcript variant X7	XM_005252223.1:c.184-59987=	XM_005252223.1:c.184-59987C>T
TRPM3 transcript variant X8	XM_005252224.1:c.184-59987=	XM_005252224.1:c.184-59987C>T
TRPM3 transcript variant X9	XM_005252225.1:c.178-59987=	XM_005252225.1:c.178-59987C>T
TRPM3 transcript variant X10	XM_005252226.1:c.178-59987=	XM_005252226.1:c.178-59987C>T
TRPM3 transcript variant X11	XM_005252227.1:c.178-59987=	XM_005252227.1:c.178-59987C>T
TRPM3 transcript variant X12	XM_005252228.1:c.184-59987=	XM_005252228.1:c.184-59987C>T
TRPM3 transcript variant X13	XM_005252229.1:c.184-59987=	XM_005252229.1:c.184-59987C>T
TRPM3 transcript variant X14	XM_005252230.1:c.178-59987=	XM_005252230.1:c.178-59987C>T
TRPM3 transcript variant X15	XM_005252231.1:c.178-59987=	XM_005252231.1:c.178-59987C>T
TRPM3 transcript variant X16	XM_005252232.1:c.184-59987=	XM_005252232.1:c.184-59987C>T
TRPM3 transcript variant X17	XM_005252233.1:c.178-59987=	XM_005252233.1:c.178-59987C>T
TRPM3 transcript variant X18	XM_005252234.1:c.178-59987=	XM_005252234.1:c.178-59987C>T
TRPM3 transcript variant X19	XM_005252235.1:c.178-59987=	XM_005252235.1:c.178-59987C>T
TRPM3 transcript variant X20	XM_005252236.1:c.178-59987=	XM_005252236.1:c.178-59987C>T

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#.

14 SubSNP, 7 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	1000GENOMES	ss335557246	May 09, 2011 (134)
2	1000GENOMES	ss1333970120	Aug 21, 2014 (142)
3	WEILL_CORNELL_DGM	ss1929900298	Feb 12, 2016 (147)
4	HUMAN_LONGEVITY	ss2311392470	Dec 20, 2016 (150)
5	GNOMAD	ss2878991929	Nov 08, 2017 (151)
6	SGDP_PRJ	ss3872293618	Apr 26, 2020 (154)
7	TOPMED	ss4822488039	Apr 27, 2021 (155)
8	1000G_HIGH_COVERAGE	ss5280870120	Oct 16, 2022 (156)
9	EVA	ss5387882702	Oct 16, 2022 (156)
10	HUGCELL_USP	ss5476872295	Oct 16, 2022 (156)
11	1000G_HIGH_COVERAGE	ss5573274043	Oct 16, 2022 (156)
12	SANFORD_IMAGENETICS	ss5647523476	Oct 16, 2022 (156)
13	EVA	ss5916530388	Oct 16, 2022 (156)
14	EVA	ss5976700106	Oct 16, 2022 (156)
15	1000Genomes	NC_000009.11 - 73539414	Oct 12, 2018 (152)
16	1000Genomes_30x	NC_000009.12 - 70924498	Oct 16, 2022 (156)
17	gnomAD - Genomes	NC_000009.12 - 70924498	Apr 27, 2021 (155)
18	Qatari	NC_000009.11 - 73539414	Apr 26, 2020 (154)
19	SGDP_PRJ	NC_000009.11 - 73539414	Apr 26, 2020 (154)
20	TopMed	NC_000009.12 - 70924498	Apr 27, 2021 (155)
21	ALFA	NC_000009.12 - 70924498	Apr 27, 2021 (155)

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
46233468, 11942228, 24310598, ss335557246, ss1333970120, ss1929900298, ss2878991929, ss3872293618, ss5387882702, ss5647523476, ss5976700106	NC_000009.11:73539413:G:A	NC_000009.12:70924497:G:A	(self)
60799978, 326883644, 659865600, 1208941787, ss2311392470, ss4822488039, ss5280870120, ss5476872295, ss5573274043, ss5916530388	NC_000009.12:70924497:G:A	NC_000009.12:70924497:G:A	(self)

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

No publications for rs139731407

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.

Choose placement

dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs139731407