Name: rs3760451
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.

rs3760451

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr17:48891815 (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 / G>T
Variation Type: SNV Single Nucleotide Variation
Frequency: A=0.324123 (85792/264690, TOPMED)
A=0.28316 (15054/53164, ALFA)
A=0.19032 (5378/28258, 14KJPN) (+ 15 more)
A=0.19057 (3194/16760, 8.3KJPN)
A=0.2815 (1803/6404, 1000G_30x)
A=0.2722 (1363/5008, 1000G)
A=0.3087 (1383/4480, Estonian)
A=0.2929 (1129/3854, ALSPAC)
A=0.2907 (1078/3708, TWINSUK)
A=0.1939 (568/2930, KOREAN)
A=0.1932 (354/1832, Korea1K)
A=0.261 (260/998, GoNL)
A=0.240 (144/600, NorthernSweden)
G=0.375 (111/296, SGDP_PRJ)
A=0.366 (79/216, Qatari)
A=0.157 (33/210, Vietnamese)
A=0.25 (10/40, GENOME_DK)
G=0.32 (7/22, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: ATP5MC1 : 2KB Upstream Variant
LOC105371814 : 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	53164	G=0.71684	A=0.28316, T=0.00000
European	Sub	39400	G=0.72873	A=0.27127, T=0.00000
African	Sub	3984	G=0.7643	A=0.2357, T=0.0000
African Others	Sub	148	G=0.730	A=0.270, T=0.000
African American	Sub	3836	G=0.7656	A=0.2344, T=0.0000
Asian	Sub	410	G=0.820	A=0.180, T=0.000
East Asian	Sub	358	G=0.810	A=0.190, T=0.000
Other Asian	Sub	52	G=0.88	A=0.12, T=0.00
Latin American 1	Sub	502	G=0.707	A=0.293, T=0.000
Latin American 2	Sub	4570	G=0.5731	A=0.4269, T=0.0000
South Asian	Sub	152	G=0.855	A=0.145, T=0.000
Other	Sub	4146	G=0.7026	A=0.2974, T=0.0000

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	G=0.675877	A=0.324123
Allele Frequency Aggregator	Total	Global	53164	G=0.71684	A=0.28316, T=0.00000
Allele Frequency Aggregator	European	Sub	39400	G=0.72873	A=0.27127, T=0.00000
Allele Frequency Aggregator	Latin American 2	Sub	4570	G=0.5731	A=0.4269, T=0.0000
Allele Frequency Aggregator	Other	Sub	4146	G=0.7026	A=0.2974, T=0.0000
Allele Frequency Aggregator	African	Sub	3984	G=0.7643	A=0.2357, T=0.0000
Allele Frequency Aggregator	Latin American 1	Sub	502	G=0.707	A=0.293, T=0.000
Allele Frequency Aggregator	Asian	Sub	410	G=0.820	A=0.180, T=0.000
Allele Frequency Aggregator	South Asian	Sub	152	G=0.855	A=0.145, T=0.000
14KJPN	JAPANESE	Study-wide	28258	G=0.80968	A=0.19032
8.3KJPN	JAPANESE	Study-wide	16760	G=0.80943	A=0.19057
1000Genomes_30x	Global	Study-wide	6404	G=0.7185	A=0.2815
1000Genomes_30x	African	Sub	1786	G=0.6607	A=0.3393
1000Genomes_30x	Europe	Sub	1266	G=0.7188	A=0.2812
1000Genomes_30x	South Asian	Sub	1202	G=0.8136	A=0.1864
1000Genomes_30x	East Asian	Sub	1170	G=0.8274	A=0.1726
1000Genomes_30x	American	Sub	980	G=0.577	A=0.423
1000Genomes	Global	Study-wide	5008	G=0.7278	A=0.2722
1000Genomes	African	Sub	1322	G=0.6702	A=0.3298
1000Genomes	East Asian	Sub	1008	G=0.8254	A=0.1746
1000Genomes	Europe	Sub	1006	G=0.7256	A=0.2744
1000Genomes	South Asian	Sub	978	G=0.813	A=0.187
1000Genomes	American	Sub	694	G=0.579	A=0.421
Genetic variation in the Estonian population	Estonian	Study-wide	4480	G=0.6913	A=0.3087
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.7071	A=0.2929
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.7093	A=0.2907
KOREAN population from KRGDB	KOREAN	Study-wide	2930	G=0.8061	A=0.1939
Korean Genome Project	KOREAN	Study-wide	1832	G=0.8068	A=0.1932
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	G=0.739	A=0.261
Northern Sweden	ACPOP	Study-wide	600	G=0.760	A=0.240
SGDP_PRJ	Global	Study-wide	296	G=0.375	A=0.625
Qatari	Global	Study-wide	216	G=0.634	A=0.366
A Vietnamese Genetic Variation Database	Global	Study-wide	210	G=0.843	A=0.157
The Danish reference pan genome	Danish	Study-wide	40	G=0.75	A=0.25
Siberian	Global	Study-wide	22	G=0.32	A=0.68

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 17	NC_000017.11:g.48891815G>A
GRCh38.p14 chr 17	NC_000017.11:g.48891815G>T
GRCh37.p13 chr 17	NC_000017.10:g.46969177G>A
GRCh37.p13 chr 17	NC_000017.10:g.46969177G>T

Gene: ATP5MC1, ATP synthase membrane subunit c locus 1 (plus strand) : 2KB Upstream Variant

Molecule type	Change	Amino acid[Codon]	SO Term
ATP5MC1 transcript variant 2	NM_001002027.2:c.	N/A	Upstream Transcript Variant
ATP5MC1 transcript variant 1	NM_005175.3:c.	N/A	Upstream Transcript Variant

Gene: LOC105371814, uncharacterized LOC105371814 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC105371814 transcript	NR_135674.1: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	G=	A	T
GRCh38.p14 chr 17	NC_000017.11:g.48891815=	NC_000017.11:g.48891815G>A	NC_000017.11:g.48891815G>T
GRCh37.p13 chr 17	NC_000017.10:g.46969177=	NC_000017.10:g.46969177G>A	NC_000017.10:g.46969177G>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#.

81 SubSNP, 20 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	YUSUKE	ss4946484	Aug 28, 2002 (107)
2	BCM_SSAHASNP	ss10877645	Jul 11, 2003 (116)
3	ABI	ss44037801	Mar 14, 2006 (126)
4	HGSV	ss78662247	Dec 06, 2007 (129)
5	HUMANGENOME_JCVI	ss96598171	Feb 05, 2009 (130)
6	1000GENOMES	ss109789969	Jan 24, 2009 (130)
7	1000GENOMES	ss113583441	Jan 25, 2009 (130)
8	ENSEMBL	ss132613154	Dec 01, 2009 (131)
9	GMI	ss158067625	Dec 01, 2009 (131)
10	ILLUMINA	ss160637862	Dec 01, 2009 (131)
11	COMPLETE_GENOMICS	ss168247165	Jul 04, 2010 (132)
12	COMPLETE_GENOMICS	ss169726732	Jul 04, 2010 (132)
13	COMPLETE_GENOMICS	ss171489079	Jul 04, 2010 (132)
14	BCM-HGSC-SUB	ss207789943	Jul 04, 2010 (132)
15	1000GENOMES	ss227563775	Jul 14, 2010 (132)
16	1000GENOMES	ss237257862	Jul 15, 2010 (132)
17	1000GENOMES	ss243550786	Jul 15, 2010 (132)
18	GMI	ss282779178	May 04, 2012 (137)
19	PJP	ss292059593	May 09, 2011 (134)
20	ILLUMINA	ss481766234	Sep 08, 2015 (146)
21	ILLUMINA	ss483228718	May 04, 2012 (137)
22	ILLUMINA	ss483632912	May 04, 2012 (137)
23	ILLUMINA	ss535447745	Sep 08, 2015 (146)
24	TISHKOFF	ss565294721	Apr 25, 2013 (138)
25	SSMP	ss661102257	Apr 25, 2013 (138)
26	ILLUMINA	ss780199094	Sep 08, 2015 (146)
27	ILLUMINA	ss782057807	Sep 08, 2015 (146)
28	ILLUMINA	ss835683652	Sep 08, 2015 (146)
29	EVA-GONL	ss993148582	Aug 21, 2014 (142)
30	JMKIDD_LAB	ss1081084316	Aug 21, 2014 (142)
31	1000GENOMES	ss1358813422	Aug 21, 2014 (142)
32	DDI	ss1428043426	Apr 01, 2015 (144)
33	EVA_GENOME_DK	ss1578173686	Apr 01, 2015 (144)
34	EVA_UK10K_ALSPAC	ss1635727678	Apr 01, 2015 (144)
35	EVA_UK10K_TWINSUK	ss1678721711	Apr 01, 2015 (144)
36	EVA_DECODE	ss1697191511	Apr 01, 2015 (144)
37	HAMMER_LAB	ss1808800220	Sep 08, 2015 (146)
38	WEILL_CORNELL_DGM	ss1936610813	Feb 12, 2016 (147)
39	GENOMED	ss1968397367	Jul 19, 2016 (147)
40	JJLAB	ss2029081632	Sep 14, 2016 (149)
41	USC_VALOUEV	ss2157556680	Dec 20, 2016 (150)
42	HUMAN_LONGEVITY	ss2217144003	Dec 20, 2016 (150)
43	ILLUMINA	ss2633401187	Nov 08, 2017 (151)
44	GRF	ss2702116524	Nov 08, 2017 (151)
45	GNOMAD	ss2950362356	Nov 08, 2017 (151)
46	SWEGEN	ss3015607659	Nov 08, 2017 (151)
47	BIOINF_KMB_FNS_UNIBA	ss3028362482	Nov 08, 2017 (151)
48	CSHL	ss3351761931	Nov 08, 2017 (151)
49	ILLUMINA	ss3627678969	Oct 12, 2018 (152)
50	ILLUMINA	ss3631381968	Oct 12, 2018 (152)
51	ILLUMINA	ss3636367168	Oct 12, 2018 (152)
52	ILLUMINA	ss3641994376	Oct 12, 2018 (152)
53	URBANLAB	ss3650664655	Oct 12, 2018 (152)
54	EGCUT_WGS	ss3682481363	Jul 13, 2019 (153)
55	EVA_DECODE	ss3700549685	Jul 13, 2019 (153)
56	ACPOP	ss3742061750	Jul 13, 2019 (153)
57	EVA	ss3754715213	Jul 13, 2019 (153)
58	PACBIO	ss3788218883	Jul 13, 2019 (153)
59	PACBIO	ss3793173769	Jul 13, 2019 (153)
60	PACBIO	ss3798059529	Jul 13, 2019 (153)
61	KHV_HUMAN_GENOMES	ss3819982396	Jul 13, 2019 (153)
62	EVA	ss3834888983	Apr 27, 2020 (154)
63	EVA	ss3841056703	Apr 27, 2020 (154)
64	EVA	ss3846553683	Apr 27, 2020 (154)
65	SGDP_PRJ	ss3885837392	Apr 27, 2020 (154)
66	KRGDB	ss3935547875	Apr 27, 2020 (154)
67	KOGIC	ss3978920794	Apr 27, 2020 (154)
68	TOPMED	ss5037404011	Apr 26, 2021 (155)
69	TOMMO_GENOMICS	ss5222626268	Apr 26, 2021 (155)
70	1000G_HIGH_COVERAGE	ss5303280372	Oct 16, 2022 (156)
71	EVA	ss5315889163	Oct 16, 2022 (156)
72	HUGCELL_USP	ss5496312845	Oct 16, 2022 (156)
73	EVA	ss5511779758	Oct 16, 2022 (156)
74	1000G_HIGH_COVERAGE	ss5607069786	Oct 16, 2022 (156)
75	SANFORD_IMAGENETICS	ss5660184187	Oct 16, 2022 (156)
76	TOMMO_GENOMICS	ss5778904143	Oct 16, 2022 (156)
77	YY_MCH	ss5816576084	Oct 16, 2022 (156)
78	EVA	ss5834041955	Oct 16, 2022 (156)
79	EVA	ss5851822500	Oct 16, 2022 (156)
80	EVA	ss5914091929	Oct 16, 2022 (156)
81	EVA	ss5951572754	Oct 16, 2022 (156)
82	1000Genomes	NC_000017.10 - 46969177	Oct 12, 2018 (152)
83	1000Genomes_30x	NC_000017.11 - 48891815	Oct 16, 2022 (156)
84	The Avon Longitudinal Study of Parents and Children	NC_000017.10 - 46969177	Oct 12, 2018 (152)
85	Genetic variation in the Estonian population	NC_000017.10 - 46969177	Oct 12, 2018 (152)
86	The Danish reference pan genome	NC_000017.10 - 46969177	Apr 27, 2020 (154)
87	gnomAD - Genomes Submission ignored due to conflicting rows: Row 508486412 (NC_000017.11:48891814:G:A 44045/139878) Row 508486413 (NC_000017.11:48891814:G:T 1/139930)	-	Apr 26, 2021 (155)
88	gnomAD - Genomes Submission ignored due to conflicting rows: Row 508486412 (NC_000017.11:48891814:G:A 44045/139878) Row 508486413 (NC_000017.11:48891814:G:T 1/139930)	-	Apr 26, 2021 (155)
89	Genome of the Netherlands Release 5	NC_000017.10 - 46969177	Apr 27, 2020 (154)
90	KOREAN population from KRGDB	NC_000017.10 - 46969177	Apr 27, 2020 (154)
91	Korean Genome Project	NC_000017.11 - 48891815	Apr 27, 2020 (154)
92	Northern Sweden	NC_000017.10 - 46969177	Jul 13, 2019 (153)
93	Qatari	NC_000017.10 - 46969177	Apr 27, 2020 (154)
94	SGDP_PRJ	NC_000017.10 - 46969177	Apr 27, 2020 (154)
95	Siberian	NC_000017.10 - 46969177	Apr 27, 2020 (154)
96	8.3KJPN	NC_000017.10 - 46969177	Apr 26, 2021 (155)
97	14KJPN	NC_000017.11 - 48891815	Oct 16, 2022 (156)
98	TopMed	NC_000017.11 - 48891815	Apr 26, 2021 (155)
99	UK 10K study - Twins	NC_000017.10 - 46969177	Oct 12, 2018 (152)
100	A Vietnamese Genetic Variation Database	NC_000017.10 - 46969177	Jul 13, 2019 (153)
101	ALFA	NC_000017.11 - 48891815	Apr 26, 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
ss78662247, ss109789969, ss113583441, ss168247165, ss169726732, ss171489079, ss207789943, ss282779178, ss292059593, ss483632912, ss1697191511	NC_000017.9:44324175:G:A	NC_000017.11:48891814:G:A	(self)
72061414, 39932971, 28219611, 4375344, 17798093, 42725269, 15346615, 18652735, 37854372, 10073034, 80595575, 39932971, 8833827, ss227563775, ss237257862, ss243550786, ss481766234, ss483228718, ss535447745, ss565294721, ss661102257, ss780199094, ss782057807, ss835683652, ss993148582, ss1081084316, ss1358813422, ss1428043426, ss1578173686, ss1635727678, ss1678721711, ss1808800220, ss1936610813, ss1968397367, ss2029081632, ss2157556680, ss2633401187, ss2702116524, ss2950362356, ss3015607659, ss3351761931, ss3627678969, ss3631381968, ss3636367168, ss3641994376, ss3682481363, ss3742061750, ss3754715213, ss3788218883, ss3793173769, ss3798059529, ss3834888983, ss3841056703, ss3885837392, ss3935547875, ss5222626268, ss5315889163, ss5511779758, ss5660184187, ss5834041955, ss5951572754	NC_000017.10:46969176:G:A	NC_000017.11:48891814:G:A	(self)
94595721, 35298795, 112741247, 252949673, 8647998922, ss2217144003, ss3028362482, ss3650664655, ss3700549685, ss3819982396, ss3846553683, ss3978920794, ss5037404011, ss5303280372, ss5496312845, ss5607069786, ss5778904143, ss5816576084, ss5851822500, ss5914091929	NC_000017.11:48891814:G:A	NC_000017.11:48891814:G:A	(self)
ss10877645	NT_010783.13:2262375:G:A	NC_000017.11:48891814:G:A	(self)
ss4946484, ss44037801, ss96598171, ss132613154, ss158067625, ss160637862	NT_010783.15:12243328:G:A	NC_000017.11:48891814:G:A	(self)
8647998922	NC_000017.11:48891814:G:T	NC_000017.11:48891814:G:T	(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 rs3760451

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

rs3760451