Name: rs6083580
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.

rs6083580

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr20:2539810 (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: T>A / T>C / T>G
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.458291 (121305/264690, TOPMED)
C=0.47615 (13455/28258, 14KJPN)
C=0.45896 (7873/17154, ALFA) (+ 16 more)
C=0.47405 (7945/16760, 8.3KJPN)
T=0.4596 (2943/6404, 1000G_30x)
T=0.4543 (2275/5008, 1000G)
T=0.4808 (2154/4480, Estonian)
T=0.4712 (1816/3854, ALSPAC)
T=0.4455 (1652/3708, TWINSUK)
C=0.4239 (1242/2930, KOREAN)
C=0.4214 (772/1832, Korea1K)
T=0.476 (475/998, GoNL)
C=0.438 (263/600, NorthernSweden)
T=0.280 (117/418, SGDP_PRJ)
T=0.500 (108/216, Qatari)
C=0.500 (108/216, Qatari)
C=0.439 (94/214, Vietnamese)
C=0.38 (15/40, GENOME_DK)
T=0.27 (8/30, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: TMC2 : Intron Variant
LOC105372504 : 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	17240	T=0.54066	A=0.00000, C=0.45934, G=0.00000
European	Sub	14316	T=0.52438	A=0.00000, C=0.47562, G=0.00000
African	Sub	1844	T=0.6323	A=0.0000, C=0.3677, G=0.0000
African Others	Sub	54	T=0.70	A=0.00, C=0.30, G=0.00
African American	Sub	1790	T=0.6302	A=0.0000, C=0.3698, G=0.0000
Asian	Sub	48	T=0.96	A=0.00, C=0.04, G=0.00
East Asian	Sub	36	T=1.00	A=0.00, C=0.00, G=0.00
Other Asian	Sub	12	T=0.83	A=0.00, C=0.17, G=0.00
Latin American 1	Sub	46	T=0.87	A=0.00, C=0.13, G=0.00
Latin American 2	Sub	110	T=0.964	A=0.000, C=0.036, G=0.000
South Asian	Sub	18	T=0.83	A=0.00, C=0.17, G=0.00
Other	Sub	858	T=0.514	A=0.000, C=0.486, G=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").

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Study	Population	Group	Sample Size	Ref Allele	Alt Allele
TopMed	Global	Study-wide	264690	T=0.458291	C=0.541709
14KJPN	JAPANESE	Study-wide	28258	T=0.52385	C=0.47615
Allele Frequency Aggregator	Total	Global	17154	T=0.54104	A=0.00000, C=0.45896, G=0.00000
Allele Frequency Aggregator	European	Sub	14246	T=0.52457	A=0.00000, C=0.47543, G=0.00000
Allele Frequency Aggregator	African	Sub	1844	T=0.6323	A=0.0000, C=0.3677, G=0.0000
Allele Frequency Aggregator	Other	Sub	842	T=0.517	A=0.000, C=0.483, G=0.000
Allele Frequency Aggregator	Latin American 2	Sub	110	T=0.964	A=0.000, C=0.036, G=0.000
Allele Frequency Aggregator	Asian	Sub	48	T=0.96	A=0.00, C=0.04, G=0.00
Allele Frequency Aggregator	Latin American 1	Sub	46	T=0.87	A=0.00, C=0.13, G=0.00
Allele Frequency Aggregator	South Asian	Sub	18	T=0.83	A=0.00, C=0.17, G=0.00
8.3KJPN	JAPANESE	Study-wide	16760	T=0.52595	C=0.47405
1000Genomes_30x	Global	Study-wide	6404	T=0.4596	C=0.5404
1000Genomes_30x	African	Sub	1786	T=0.4496	C=0.5504
1000Genomes_30x	Europe	Sub	1266	T=0.4629	C=0.5371
1000Genomes_30x	South Asian	Sub	1202	T=0.3935	C=0.6065
1000Genomes_30x	East Asian	Sub	1170	T=0.5393	C=0.4607
1000Genomes_30x	American	Sub	980	T=0.459	C=0.541
1000Genomes	Global	Study-wide	5008	T=0.4543	C=0.5457
1000Genomes	African	Sub	1322	T=0.4440	C=0.5560
1000Genomes	East Asian	Sub	1008	T=0.5308	C=0.4692
1000Genomes	Europe	Sub	1006	T=0.4583	C=0.5417
1000Genomes	South Asian	Sub	978	T=0.389	C=0.611
1000Genomes	American	Sub	694	T=0.450	C=0.550
Genetic variation in the Estonian population	Estonian	Study-wide	4480	T=0.4808	C=0.5192
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.4712	C=0.5288
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.4455	C=0.5545
KOREAN population from KRGDB	KOREAN	Study-wide	2930	T=0.5761	C=0.4239
Korean Genome Project	KOREAN	Study-wide	1832	T=0.5786	C=0.4214
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.476	C=0.524
Northern Sweden	ACPOP	Study-wide	600	T=0.562	C=0.438
SGDP_PRJ	Global	Study-wide	418	T=0.280	C=0.720
Qatari	Global	Study-wide	216	T=0.500	C=0.500
A Vietnamese Genetic Variation Database	Global	Study-wide	214	T=0.561	C=0.439
The Danish reference pan genome	Danish	Study-wide	40	T=0.62	C=0.38
Siberian	Global	Study-wide	30	T=0.27	C=0.73

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 20	NC_000020.11:g.2539810T>A
GRCh38.p14 chr 20	NC_000020.11:g.2539810T>C
GRCh38.p14 chr 20	NC_000020.11:g.2539810T>G
GRCh37.p13 chr 20	NC_000020.10:g.2520456T>A
GRCh37.p13 chr 20	NC_000020.10:g.2520456T>C
GRCh37.p13 chr 20	NC_000020.10:g.2520456T>G
TMC2 RefSeqGene	NG_042834.1:g.8204T>A
TMC2 RefSeqGene	NG_042834.1:g.8204T>C
TMC2 RefSeqGene	NG_042834.1:g.8204T>G

Gene: TMC2, transmembrane channel like 2 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
TMC2 transcript	NM_080751.3:c.82+2494T>A	N/A	Intron Variant
TMC2 transcript variant X2	XM_005260660.5:c.	N/A	Genic Upstream Transcript Variant
TMC2 transcript variant X1	XR_001754152.2:n.	N/A	Genic Upstream Transcript Variant

Gene: LOC105372504, uncharacterized LOC105372504 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC105372504 transcript	XR_937204.3:n.	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.

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	T=	A	C	G
GRCh38.p14 chr 20	NC_000020.11:g.2539810=	NC_000020.11:g.2539810T>A	NC_000020.11:g.2539810T>C	NC_000020.11:g.2539810T>G
GRCh37.p13 chr 20	NC_000020.10:g.2520456=	NC_000020.10:g.2520456T>A	NC_000020.10:g.2520456T>C	NC_000020.10:g.2520456T>G
TMC2 RefSeqGene	NG_042834.1:g.8204=	NG_042834.1:g.8204T>A	NG_042834.1:g.8204T>C	NG_042834.1:g.8204T>G
TMC2 transcript	NM_080751.2:c.82+2494=	NM_080751.2:c.82+2494T>A	NM_080751.2:c.82+2494T>C	NM_080751.2:c.82+2494T>G
TMC2 transcript	NM_080751.3:c.82+2494=	NM_080751.3:c.82+2494T>A	NM_080751.3:c.82+2494T>C	NM_080751.3:c.82+2494T>G

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#.

81 SubSNP, 21 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_SNP	ss8405378	Apr 21, 2003 (114)
2	CSHL-HAPMAP	ss16897455	Feb 27, 2004 (120)
3	SSAHASNP	ss21786677	Apr 05, 2004 (121)
4	PERLEGEN	ss24492345	Sep 20, 2004 (123)
5	ABI	ss41366058	Mar 14, 2006 (126)
6	BCMHGSC_JDW	ss91617699	Mar 24, 2008 (129)
7	HUMANGENOME_JCVI	ss96209177	Feb 04, 2009 (130)
8	BGI	ss103715491	Dec 01, 2009 (131)
9	1000GENOMES	ss111618525	Jan 25, 2009 (130)
10	1000GENOMES	ss115373544	Jan 25, 2009 (130)
11	ENSEMBL	ss138199772	Dec 01, 2009 (131)
12	ENSEMBL	ss143801874	Dec 01, 2009 (131)
13	GMI	ss156085506	Dec 01, 2009 (131)
14	COMPLETE_GENOMICS	ss167679310	Jul 04, 2010 (132)
15	COMPLETE_GENOMICS	ss168889824	Jul 04, 2010 (132)
16	COMPLETE_GENOMICS	ss171827079	Jul 04, 2010 (132)
17	ILLUMINA	ss173977494	Jul 04, 2010 (132)
18	BUSHMAN	ss203810656	Jul 04, 2010 (132)
19	BCM-HGSC-SUB	ss208592962	Jul 04, 2010 (132)
20	1000GENOMES	ss228222186	Jul 14, 2010 (132)
21	1000GENOMES	ss237738226	Jul 15, 2010 (132)
22	1000GENOMES	ss243929866	Jul 15, 2010 (132)
23	BL	ss255435781	May 09, 2011 (134)
24	GMI	ss283276608	May 04, 2012 (137)
25	GMI	ss287411964	Apr 25, 2013 (138)
26	PJP	ss292564623	May 09, 2011 (134)
27	ILLUMINA	ss537337302	Sep 08, 2015 (146)
28	TISHKOFF	ss566096213	Apr 25, 2013 (138)
29	SSMP	ss661966031	Apr 25, 2013 (138)
30	EVA-GONL	ss994477281	Aug 21, 2014 (142)
31	JMKIDD_LAB	ss1082024898	Aug 21, 2014 (142)
32	1000GENOMES	ss1363839025	Aug 21, 2014 (142)
33	DDI	ss1428977210	Apr 01, 2015 (144)
34	EVA_GENOME_DK	ss1579411067	Apr 01, 2015 (144)
35	EVA_UK10K_ALSPAC	ss1638289811	Apr 01, 2015 (144)
36	EVA_UK10K_TWINSUK	ss1681283844	Apr 01, 2015 (144)
37	EVA_DECODE	ss1698531450	Apr 01, 2015 (144)
38	HAMMER_LAB	ss1809393848	Sep 08, 2015 (146)
39	WEILL_CORNELL_DGM	ss1937986194	Feb 12, 2016 (147)
40	GENOMED	ss1969076000	Jul 19, 2016 (147)
41	JJLAB	ss2029769546	Sep 14, 2016 (149)
42	USC_VALOUEV	ss2158323368	Dec 20, 2016 (150)
43	HUMAN_LONGEVITY	ss2240860578	Dec 20, 2016 (150)
44	SYSTEMSBIOZJU	ss2629382270	Nov 08, 2017 (151)
45	GRF	ss2703994921	Nov 08, 2017 (151)
46	GNOMAD	ss2964801481	Nov 08, 2017 (151)
47	AFFY	ss2985207635	Nov 08, 2017 (151)
48	AFFY	ss2985828387	Nov 08, 2017 (151)
49	SWEGEN	ss3017773785	Nov 08, 2017 (151)
50	BIOINF_KMB_FNS_UNIBA	ss3028716692	Nov 08, 2017 (151)
51	CSHL	ss3352389961	Nov 08, 2017 (151)
52	ILLUMINA	ss3628336271	Oct 12, 2018 (152)
53	ILLUMINA	ss3638330963	Oct 12, 2018 (152)
54	URBANLAB	ss3650957487	Oct 12, 2018 (152)
55	ILLUMINA	ss3653975844	Oct 12, 2018 (152)
56	EGCUT_WGS	ss3684487720	Jul 13, 2019 (153)
57	EVA_DECODE	ss3706443205	Jul 13, 2019 (153)
58	ACPOP	ss3743196433	Jul 13, 2019 (153)
59	EVA	ss3758350623	Jul 13, 2019 (153)
60	PACBIO	ss3788582935	Jul 13, 2019 (153)
61	PACBIO	ss3793485640	Jul 13, 2019 (153)
62	PACBIO	ss3798372760	Jul 13, 2019 (153)
63	KHV_HUMAN_GENOMES	ss3821522439	Jul 13, 2019 (153)
64	EVA	ss3835555817	Apr 27, 2020 (154)
65	EVA	ss3841401497	Apr 27, 2020 (154)
66	EVA	ss3846908872	Apr 27, 2020 (154)
67	SGDP_PRJ	ss3888610557	Apr 27, 2020 (154)
68	KRGDB	ss3938789144	Apr 27, 2020 (154)
69	KOGIC	ss3981714944	Apr 27, 2020 (154)
70	TOPMED	ss5080338810	Apr 27, 2021 (155)
71	TOMMO_GENOMICS	ss5228585473	Apr 27, 2021 (155)
72	1000G_HIGH_COVERAGE	ss5307884800	Oct 13, 2022 (156)
73	HUGCELL_USP	ss5500305123	Oct 13, 2022 (156)
74	1000G_HIGH_COVERAGE	ss5613870610	Oct 13, 2022 (156)
75	SANFORD_IMAGENETICS	ss5662748890	Oct 13, 2022 (156)
76	TOMMO_GENOMICS	ss5787500679	Oct 13, 2022 (156)
77	YY_MCH	ss5817764985	Oct 13, 2022 (156)
78	EVA	ss5845363502	Oct 13, 2022 (156)
79	EVA	ss5853042659	Oct 13, 2022 (156)
80	EVA	ss5922445992	Oct 13, 2022 (156)
81	EVA	ss5957646736	Oct 13, 2022 (156)
82	1000Genomes	NC_000020.10 - 2520456	Oct 12, 2018 (152)
83	1000Genomes_30x	NC_000020.11 - 2539810	Oct 13, 2022 (156)
84	The Avon Longitudinal Study of Parents and Children	NC_000020.10 - 2520456	Oct 12, 2018 (152)
85	Genetic variation in the Estonian population	NC_000020.10 - 2520456	Oct 12, 2018 (152)
86	The Danish reference pan genome	NC_000020.10 - 2520456	Apr 27, 2020 (154)
87	gnomAD - Genomes Submission ignored due to conflicting rows: Row 544881015 (NC_000020.11:2539809:T:A 1/139938) Row 544881016 (NC_000020.11:2539809:T:C 74982/139838) Row 544881017 (NC_000020.11:2539809:T:G 2/139938)	-	Apr 27, 2021 (155)
88	gnomAD - Genomes Submission ignored due to conflicting rows: Row 544881015 (NC_000020.11:2539809:T:A 1/139938) Row 544881016 (NC_000020.11:2539809:T:C 74982/139838) Row 544881017 (NC_000020.11:2539809:T:G 2/139938)	-	Apr 27, 2021 (155)
89	gnomAD - Genomes Submission ignored due to conflicting rows: Row 544881015 (NC_000020.11:2539809:T:A 1/139938) Row 544881016 (NC_000020.11:2539809:T:C 74982/139838) Row 544881017 (NC_000020.11:2539809:T:G 2/139938)	-	Apr 27, 2021 (155)
90	Genome of the Netherlands Release 5	NC_000020.10 - 2520456	Apr 27, 2020 (154)
91	KOREAN population from KRGDB	NC_000020.10 - 2520456	Apr 27, 2020 (154)
92	Korean Genome Project	NC_000020.11 - 2539810	Apr 27, 2020 (154)
93	Northern Sweden	NC_000020.10 - 2520456	Jul 13, 2019 (153)
94	Qatari	NC_000020.10 - 2520456	Apr 27, 2020 (154)
95	SGDP_PRJ	NC_000020.10 - 2520456	Apr 27, 2020 (154)
96	Siberian	NC_000020.10 - 2520456	Apr 27, 2020 (154)
97	8.3KJPN	NC_000020.10 - 2520456	Apr 27, 2021 (155)
98	14KJPN	NC_000020.11 - 2539810	Oct 13, 2022 (156)
99	TopMed	NC_000020.11 - 2539810	Apr 27, 2021 (155)
100	UK 10K study - Twins	NC_000020.10 - 2520456	Oct 12, 2018 (152)
101	A Vietnamese Genetic Variation Database	NC_000020.10 - 2520456	Jul 13, 2019 (153)
102	ALFA	NC_000020.11 - 2539810	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).

Associated ID	History Updated (Build)
rs17761045	Oct 07, 2004 (123)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
10144476981	NC_000020.11:2539809:T:A	NC_000020.11:2539809:T:A	(self)
ss91617699, ss111618525, ss115373544, ss167679310, ss168889824, ss171827079, ss203810656, ss208592962, ss255435781, ss283276608, ss287411964, ss292564623, ss1698531450	NC_000020.9:2468455:T:C	NC_000020.11:2539809:T:C	(self)
77270530, 42770126, 30225968, 5576006, 19057331, 45966538, 16481298, 20028116, 40627537, 10839722, 86554780, 42770126, 9441783, ss228222186, ss237738226, ss243929866, ss537337302, ss566096213, ss661966031, ss994477281, ss1082024898, ss1363839025, ss1428977210, ss1579411067, ss1638289811, ss1681283844, ss1809393848, ss1937986194, ss1969076000, ss2029769546, ss2158323368, ss2629382270, ss2703994921, ss2964801481, ss2985207635, ss2985828387, ss3017773785, ss3352389961, ss3628336271, ss3638330963, ss3653975844, ss3684487720, ss3743196433, ss3758350623, ss3788582935, ss3793485640, ss3798372760, ss3835555817, ss3841401497, ss3888610557, ss3938789144, ss5228585473, ss5662748890, ss5845363502, ss5957646736	NC_000020.10:2520455:T:C	NC_000020.11:2539809:T:C	(self)
101396545, 38092945, 121337783, 355447755, 10144476981, ss2240860578, ss3028716692, ss3650957487, ss3706443205, ss3821522439, ss3846908872, ss3981714944, ss5080338810, ss5307884800, ss5500305123, ss5613870610, ss5787500679, ss5817764985, ss5853042659, ss5922445992	NC_000020.11:2539809:T:C	NC_000020.11:2539809:T:C	(self)
ss8405378, ss16897455, ss21786677, ss24492345, ss41366058, ss96209177, ss103715491, ss138199772, ss143801874, ss156085506, ss173977494	NT_011387.8:2460455:T:C	NC_000020.11:2539809:T:C	(self)
10144476981	NC_000020.11:2539809:T:G	NC_000020.11:2539809:T:G	(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 rs6083580

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.

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dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs6083580