Name: rs56166107
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.

rs56166107

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr19:49202383 (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=0.263897 (69851/264690, TOPMED)
A=0.258877 (36191/139800, GnomAD)
A=0.14845 (4195/28258, 14KJPN) (+ 16 more)
A=0.26808 (5064/18890, ALFA)
A=0.14952 (2506/16760, 8.3KJPN)
A=0.2797 (1791/6404, 1000G_30x)
A=0.2849 (1427/5008, 1000G)
A=0.2065 (925/4480, Estonian)
A=0.2898 (1117/3854, ALSPAC)
A=0.3015 (1118/3708, TWINSUK)
A=0.2130 (624/2930, KOREAN)
A=0.2085 (382/1832, Korea1K)
A=0.268 (267/998, GoNL)
A=0.308 (185/600, NorthernSweden)
G=0.415 (108/260, SGDP_PRJ)
A=0.292 (63/216, Qatari)
A=0.241 (51/212, Vietnamese)
A=0.30 (12/40, GENOME_DK)
G=0.47 (14/30, Siberian)

Clinical Significance: Reported in ClinVar
Gene : Consequence: TRPM4 : 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	18890	G=0.73192	A=0.26808
European	Sub	14286	G=0.72281	A=0.27719
African	Sub	2946	G=0.7756	A=0.2244
African Others	Sub	114	G=0.772	A=0.228
African American	Sub	2832	G=0.7758	A=0.2242
Asian	Sub	112	G=0.750	A=0.250
East Asian	Sub	86	G=0.72	A=0.28
Other Asian	Sub	26	G=0.85	A=0.15
Latin American 1	Sub	146	G=0.692	A=0.308
Latin American 2	Sub	610	G=0.775	A=0.225
South Asian	Sub	98	G=0.54	A=0.46
Other	Sub	692	G=0.728	A=0.272

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=0.736103	A=0.263897
gnomAD - Genomes	Global	Study-wide	139800	G=0.741123	A=0.258877
gnomAD - Genomes	European	Sub	75772	G=0.71874	A=0.28126
gnomAD - Genomes	African	Sub	41848	G=0.77949	A=0.22051
gnomAD - Genomes	American	Sub	13592	G=0.77994	A=0.22006
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	G=0.6137	A=0.3863
gnomAD - Genomes	East Asian	Sub	3118	G=0.7534	A=0.2466
gnomAD - Genomes	Other	Sub	2146	G=0.7171	A=0.2829
14KJPN	JAPANESE	Study-wide	28258	G=0.85155	A=0.14845
Allele Frequency Aggregator	Total	Global	18890	G=0.73192	A=0.26808
Allele Frequency Aggregator	European	Sub	14286	G=0.72281	A=0.27719
Allele Frequency Aggregator	African	Sub	2946	G=0.7756	A=0.2244
Allele Frequency Aggregator	Other	Sub	692	G=0.728	A=0.272
Allele Frequency Aggregator	Latin American 2	Sub	610	G=0.775	A=0.225
Allele Frequency Aggregator	Latin American 1	Sub	146	G=0.692	A=0.308
Allele Frequency Aggregator	Asian	Sub	112	G=0.750	A=0.250
Allele Frequency Aggregator	South Asian	Sub	98	G=0.54	A=0.46
8.3KJPN	JAPANESE	Study-wide	16760	G=0.85048	A=0.14952
1000Genomes_30x	Global	Study-wide	6404	G=0.7203	A=0.2797
1000Genomes_30x	African	Sub	1786	G=0.7721	A=0.2279
1000Genomes_30x	Europe	Sub	1266	G=0.6872	A=0.3128
1000Genomes_30x	South Asian	Sub	1202	G=0.5757	A=0.4243
1000Genomes_30x	East Asian	Sub	1170	G=0.7624	A=0.2376
1000Genomes_30x	American	Sub	980	G=0.796	A=0.204
1000Genomes	Global	Study-wide	5008	G=0.7151	A=0.2849
1000Genomes	African	Sub	1322	G=0.7738	A=0.2262
1000Genomes	East Asian	Sub	1008	G=0.7540	A=0.2460
1000Genomes	Europe	Sub	1006	G=0.6849	A=0.3151
1000Genomes	South Asian	Sub	978	G=0.567	A=0.433
1000Genomes	American	Sub	694	G=0.798	A=0.202
Genetic variation in the Estonian population	Estonian	Study-wide	4480	G=0.7935	A=0.2065
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.7102	A=0.2898
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.6985	A=0.3015
KOREAN population from KRGDB	KOREAN	Study-wide	2930	G=0.7870	A=0.2130
Korean Genome Project	KOREAN	Study-wide	1832	G=0.7915	A=0.2085
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	G=0.732	A=0.268
Northern Sweden	ACPOP	Study-wide	600	G=0.692	A=0.308
SGDP_PRJ	Global	Study-wide	260	G=0.415	A=0.585
Qatari	Global	Study-wide	216	G=0.708	A=0.292
A Vietnamese Genetic Variation Database	Global	Study-wide	212	G=0.759	A=0.241
The Danish reference pan genome	Danish	Study-wide	40	G=0.70	A=0.30
Siberian	Global	Study-wide	30	G=0.47	A=0.53

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 19	NC_000019.10:g.49202383G>A
GRCh37.p13 chr 19	NC_000019.9:g.49705640G>A
TRPM4 RefSeqGene	NG_027551.2:g.49625G>A

Gene: TRPM4, transient receptor potential cation channel subfamily M member 4 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
TRPM4 transcript variant 2	NM_001195227.2:c.2696+242… NM_001195227.2:c.2696+242G>A	N/A	Intron Variant
TRPM4 transcript variant 3	NM_001321281.2:c.2786+242… NM_001321281.2:c.2786+242G>A	N/A	Intron Variant
TRPM4 transcript variant 4	NM_001321282.2:c.1523+242… NM_001321282.2:c.1523+242G>A	N/A	Intron Variant
TRPM4 transcript variant 5	NM_001321283.2:c.2609+242… NM_001321283.2:c.2609+242G>A	N/A	Intron Variant
TRPM4 transcript variant 6	NM_001321285.2:c.2069+242… NM_001321285.2:c.2069+242G>A	N/A	Intron Variant
TRPM4 transcript variant 1	NM_017636.4:c.3131+242G>A	N/A	Intron Variant
TRPM4 transcript variant X1	XM_047438992.1:c.3602+242… XM_047438992.1:c.3602+242G>A	N/A	Intron Variant
TRPM4 transcript variant X2	XM_047438993.1:c.1844+242… XM_047438993.1:c.1844+242G>A	N/A	Intron 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.

Allele: A (allele ID: 1249027 )

ClinVar Accession	Disease Names	Clinical Significance
RCV001670788.2	not provided	Benign

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 19	NC_000019.10:g.49202383=	NC_000019.10:g.49202383G>A
GRCh37.p13 chr 19	NC_000019.9:g.49705640=	NC_000019.9:g.49705640G>A
TRPM4 RefSeqGene	NG_027551.2:g.49625=	NG_027551.2:g.49625G>A
TRPM4 transcript variant 2	NM_001195227.1:c.2696+242=	NM_001195227.1:c.2696+242G>A
TRPM4 transcript variant 2	NM_001195227.2:c.2696+242=	NM_001195227.2:c.2696+242G>A
TRPM4 transcript variant 3	NM_001321281.2:c.2786+242=	NM_001321281.2:c.2786+242G>A
TRPM4 transcript variant 4	NM_001321282.2:c.1523+242=	NM_001321282.2:c.1523+242G>A
TRPM4 transcript variant 5	NM_001321283.2:c.2609+242=	NM_001321283.2:c.2609+242G>A
TRPM4 transcript variant 6	NM_001321285.2:c.2069+242=	NM_001321285.2:c.2069+242G>A
TRPM4 transcript variant 1	NM_017636.3:c.3131+242=	NM_017636.3:c.3131+242G>A
TRPM4 transcript variant 1	NM_017636.4:c.3131+242=	NM_017636.4:c.3131+242G>A
TRPM4 transcript variant X1	XM_005259015.1:c.2609+242=	XM_005259015.1:c.2609+242G>A
TRPM4 transcript variant X2	XM_005259016.1:c.2069+242=	XM_005259016.1:c.2069+242G>A
TRPM4 transcript variant X1	XM_005259017.1:c.1844+242=	XM_005259017.1:c.1844+242G>A
TRPM4 transcript variant X4	XM_005259018.1:c.1523+242=	XM_005259018.1:c.1523+242G>A
TRPM4 transcript variant X1	XM_047438992.1:c.3602+242=	XM_047438992.1:c.3602+242G>A
TRPM4 transcript variant X2	XM_047438993.1:c.1844+242=	XM_047438993.1:c.1844+242G>A

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#.

61 SubSNP, 19 Frequency, 1 ClinVar submissions

No	Submitter	Submission ID	Date (Build)
1	HGSV	ss77617769	Dec 07, 2007 (129)
2	1000GENOMES	ss111466210	Jan 25, 2009 (130)
3	1000GENOMES	ss115227629	Jan 25, 2009 (130)
4	ENSEMBL	ss143182163	Dec 01, 2009 (131)
5	BUSHMAN	ss203775859	Jul 04, 2010 (132)
6	BCM-HGSC-SUB	ss208485893	Jul 04, 2010 (132)
7	1000GENOMES	ss228170649	Jul 14, 2010 (132)
8	1000GENOMES	ss237699885	Jul 15, 2010 (132)
9	1000GENOMES	ss243900573	Jul 15, 2010 (132)
10	GMI	ss283235724	May 04, 2012 (137)
11	PJP	ss292189299	May 09, 2011 (134)
12	TISHKOFF	ss566028290	Apr 25, 2013 (138)
13	SSMP	ss661895152	Apr 25, 2013 (138)
14	EVA-GONL	ss994372514	Aug 21, 2014 (142)
15	JMKIDD_LAB	ss1081952529	Aug 21, 2014 (142)
16	1000GENOMES	ss1363457801	Aug 21, 2014 (142)
17	DDI	ss1428423285	Apr 01, 2015 (144)
18	EVA_GENOME_DK	ss1578666932	Apr 01, 2015 (144)
19	EVA_UK10K_ALSPAC	ss1638103802	Apr 01, 2015 (144)
20	EVA_UK10K_TWINSUK	ss1681097835	Apr 01, 2015 (144)
21	EVA_DECODE	ss1698427507	Apr 01, 2015 (144)
22	HAMMER_LAB	ss1809341495	Sep 08, 2015 (146)
23	WEILL_CORNELL_DGM	ss1937872527	Feb 12, 2016 (147)
24	JJLAB	ss2029711778	Sep 14, 2016 (149)
25	USC_VALOUEV	ss2158259178	Dec 20, 2016 (150)
26	HUMAN_LONGEVITY	ss2226275450	Dec 20, 2016 (150)
27	SYSTEMSBIOZJU	ss2629353094	Nov 08, 2017 (151)
28	GRF	ss2702872115	Nov 08, 2017 (151)
29	GNOMAD	ss2963723217	Nov 08, 2017 (151)
30	SWEGEN	ss3017600828	Nov 08, 2017 (151)
31	BIOINF_KMB_FNS_UNIBA	ss3028686480	Nov 08, 2017 (151)
32	CSHL	ss3352336849	Nov 08, 2017 (151)
33	URBANLAB	ss3650932792	Oct 12, 2018 (152)
34	EGCUT_WGS	ss3684339565	Jul 13, 2019 (153)
35	EVA_DECODE	ss3702915331	Jul 13, 2019 (153)
36	ACPOP	ss3743102791	Jul 13, 2019 (153)
37	EVA	ss3756149929	Jul 13, 2019 (153)
38	PACBIO	ss3788551807	Jul 13, 2019 (153)
39	PACBIO	ss3793458272	Jul 13, 2019 (153)
40	PACBIO	ss3798345153	Jul 13, 2019 (153)
41	KHV_HUMAN_GENOMES	ss3821399171	Jul 13, 2019 (153)
42	EVA	ss3835499086	Apr 27, 2020 (154)
43	EVA	ss3841372318	Apr 27, 2020 (154)
44	EVA	ss3846878654	Apr 27, 2020 (154)
45	SGDP_PRJ	ss3888380498	Apr 27, 2020 (154)
46	KRGDB	ss3938526744	Apr 27, 2020 (154)
47	KOGIC	ss3981519130	Apr 27, 2020 (154)
48	TOPMED	ss5077267678	Apr 26, 2021 (155)
49	TOMMO_GENOMICS	ss5228119897	Apr 26, 2021 (155)
50	1000G_HIGH_COVERAGE	ss5307523501	Oct 16, 2022 (156)
51	EVA	ss5435299690	Oct 16, 2022 (156)
52	HUGCELL_USP	ss5499998922	Oct 16, 2022 (156)
53	1000G_HIGH_COVERAGE	ss5613367977	Oct 16, 2022 (156)
54	SANFORD_IMAGENETICS	ss5662543907	Oct 16, 2022 (156)
55	TOMMO_GENOMICS	ss5786876056	Oct 16, 2022 (156)
56	YY_MCH	ss5817666661	Oct 16, 2022 (156)
57	EVA	ss5840654214	Oct 16, 2022 (156)
58	EVA	ss5852316651	Oct 16, 2022 (156)
59	EVA	ss5928387080	Oct 16, 2022 (156)
60	EVA	ss5953950184	Oct 16, 2022 (156)
61	EVA	ss5981061531	Oct 16, 2022 (156)
62	1000Genomes	NC_000019.9 - 49705640	Oct 12, 2018 (152)
63	1000Genomes_30x	NC_000019.10 - 49202383	Oct 16, 2022 (156)
64	The Avon Longitudinal Study of Parents and Children	NC_000019.9 - 49705640	Oct 12, 2018 (152)
65	Genetic variation in the Estonian population	NC_000019.9 - 49705640	Oct 12, 2018 (152)
66	The Danish reference pan genome	NC_000019.9 - 49705640	Apr 27, 2020 (154)
67	gnomAD - Genomes	NC_000019.10 - 49202383	Apr 26, 2021 (155)
68	Genome of the Netherlands Release 5	NC_000019.9 - 49705640	Apr 27, 2020 (154)
69	KOREAN population from KRGDB	NC_000019.9 - 49705640	Apr 27, 2020 (154)
70	Korean Genome Project	NC_000019.10 - 49202383	Apr 27, 2020 (154)
71	Northern Sweden	NC_000019.9 - 49705640	Jul 13, 2019 (153)
72	Qatari	NC_000019.9 - 49705640	Apr 27, 2020 (154)
73	SGDP_PRJ	NC_000019.9 - 49705640	Apr 27, 2020 (154)
74	Siberian	NC_000019.9 - 49705640	Apr 27, 2020 (154)
75	8.3KJPN	NC_000019.9 - 49705640	Apr 26, 2021 (155)
76	14KJPN	NC_000019.10 - 49202383	Oct 16, 2022 (156)
77	TopMed	NC_000019.10 - 49202383	Apr 26, 2021 (155)
78	UK 10K study - Twins	NC_000019.9 - 49705640	Oct 12, 2018 (152)
79	A Vietnamese Genetic Variation Database	NC_000019.9 - 49705640	Jul 13, 2019 (153)
80	ALFA	NC_000019.10 - 49202383	Apr 26, 2021 (155)
81	ClinVar	RCV001670788.2	Oct 16, 2022 (156)

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
ss77617769, ss111466210, ss115227629, ss203775859, ss208485893, ss283235724, ss292189299, ss1698427507	NC_000019.8:54397451:G:A	NC_000019.10:49202382:G:A	(self)
76875460, 42562153, 30077813, 4848362, 18960508, 45704138, 16387656, 19914449, 40397478, 10775532, 86089204, 42562153, 9396840, ss228170649, ss237699885, ss243900573, ss566028290, ss661895152, ss994372514, ss1081952529, ss1363457801, ss1428423285, ss1578666932, ss1638103802, ss1681097835, ss1809341495, ss1937872527, ss2029711778, ss2158259178, ss2629353094, ss2702872115, ss2963723217, ss3017600828, ss3352336849, ss3684339565, ss3743102791, ss3756149929, ss3788551807, ss3793458272, ss3798345153, ss3835499086, ss3841372318, ss3888380498, ss3938526744, ss5228119897, ss5435299690, ss5662543907, ss5840654214, ss5953950184, ss5981061531	NC_000019.9:49705639:G:A	NC_000019.10:49202382:G:A	(self)
RCV001670788.2, 100893912, 542174102, 37897131, 120713160, 292813342, 9735216236, ss2226275450, ss3028686480, ss3650932792, ss3702915331, ss3821399171, ss3846878654, ss3981519130, ss5077267678, ss5307523501, ss5499998922, ss5613367977, ss5786876056, ss5817666661, ss5852316651, ss5928387080	NC_000019.10:49202382:G:A	NC_000019.10:49202382:G:A	(self)
ss143182163	NT_011109.16:21973857:G:A	NC_000019.10:49202382: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 rs56166107

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

rs56166107