Name: rs832410
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.

rs832410

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr17:48895503 (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: C>A / C>T
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.395051 (104566/264690, TOPMED)
T=0.402927 (56376/139916, GnomAD)
C=0.26891 (7599/28258, 14KJPN) (+ 18 more)
T=0.45093 (8518/18890, ALFA)
C=0.27112 (4544/16760, 8.3KJPN)
T=0.4122 (2640/6404, 1000G_30x)
T=0.4251 (2129/5008, 1000G)
C=0.4958 (2221/4480, Estonian)
C=0.4862 (1874/3854, ALSPAC)
C=0.4752 (1762/3708, TWINSUK)
C=0.2696 (790/2930, KOREAN)
C=0.2735 (501/1832, Korea1K)
C=0.473 (472/998, GoNL)
C=0.465 (279/600, NorthernSweden)
T=0.011 (6/534, MGP)
C=0.330 (120/364, SGDP_PRJ)
T=0.375 (81/216, Qatari)
C=0.335 (69/206, Vietnamese)
C=0.29 (20/70, Ancient Sardinia)
C=0.26 (12/46, Siberian)
C=0.45 (18/40, GENOME_DK)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: ATP5MC1 : Intron 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	18890	C=0.54907	T=0.45093
European	Sub	14286	C=0.48488	T=0.51512
African	Sub	2946	C=0.8571	T=0.1429
African Others	Sub	114	C=0.939	T=0.061
African American	Sub	2832	C=0.8538	T=0.1462
Asian	Sub	112	C=0.357	T=0.643
East Asian	Sub	86	C=0.33	T=0.67
Other Asian	Sub	26	C=0.46	T=0.54
Latin American 1	Sub	146	C=0.610	T=0.390
Latin American 2	Sub	610	C=0.564	T=0.436
South Asian	Sub	98	C=0.48	T=0.52
Other	Sub	692	C=0.578	T=0.422

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	C=0.604949	T=0.395051
gnomAD - Genomes	Global	Study-wide	139916	C=0.597073	T=0.402927
gnomAD - Genomes	European	Sub	75760	C=0.47313	T=0.52687
gnomAD - Genomes	African	Sub	41944	C=0.85729	T=0.14271
gnomAD - Genomes	American	Sub	13618	C=0.58724	T=0.41276
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	C=0.4922	T=0.5078
gnomAD - Genomes	East Asian	Sub	3118	C=0.2842	T=0.7158
gnomAD - Genomes	Other	Sub	2152	C=0.5664	T=0.4336
14KJPN	JAPANESE	Study-wide	28258	C=0.26891	T=0.73109
Allele Frequency Aggregator	Total	Global	18890	C=0.54907	T=0.45093
Allele Frequency Aggregator	European	Sub	14286	C=0.48488	T=0.51512
Allele Frequency Aggregator	African	Sub	2946	C=0.8571	T=0.1429
Allele Frequency Aggregator	Other	Sub	692	C=0.578	T=0.422
Allele Frequency Aggregator	Latin American 2	Sub	610	C=0.564	T=0.436
Allele Frequency Aggregator	Latin American 1	Sub	146	C=0.610	T=0.390
Allele Frequency Aggregator	Asian	Sub	112	C=0.357	T=0.643
Allele Frequency Aggregator	South Asian	Sub	98	C=0.48	T=0.52
8.3KJPN	JAPANESE	Study-wide	16760	C=0.27112	T=0.72888
1000Genomes_30x	Global	Study-wide	6404	C=0.5878	T=0.4122
1000Genomes_30x	African	Sub	1786	C=0.9367	T=0.0633
1000Genomes_30x	Europe	Sub	1266	C=0.4463	T=0.5537
1000Genomes_30x	South Asian	Sub	1202	C=0.5183	T=0.4817
1000Genomes_30x	East Asian	Sub	1170	C=0.3162	T=0.6838
1000Genomes_30x	American	Sub	980	C=0.544	T=0.456
1000Genomes	Global	Study-wide	5008	C=0.5749	T=0.4251
1000Genomes	African	Sub	1322	C=0.9342	T=0.0658
1000Genomes	East Asian	Sub	1008	C=0.3155	T=0.6845
1000Genomes	Europe	Sub	1006	C=0.4414	T=0.5586
1000Genomes	South Asian	Sub	978	C=0.514	T=0.486
1000Genomes	American	Sub	694	C=0.546	T=0.454
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.4958	T=0.5042
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.4862	T=0.5138
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.4752	T=0.5248
KOREAN population from KRGDB	KOREAN	Study-wide	2930	C=0.2696	A=0.0000, T=0.7304
Korean Genome Project	KOREAN	Study-wide	1832	C=0.2735	T=0.7265
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.473	T=0.527
Northern Sweden	ACPOP	Study-wide	600	C=0.465	T=0.535
Medical Genome Project healthy controls from Spanish population	Spanish controls	Study-wide	534	C=0.989	T=0.011
SGDP_PRJ	Global	Study-wide	364	C=0.330	T=0.670
Qatari	Global	Study-wide	216	C=0.625	T=0.375
A Vietnamese Genetic Variation Database	Global	Study-wide	206	C=0.335	T=0.665
Ancient Sardinia genome-wide 1240k capture data generation and analysis	Global	Study-wide	70	C=0.29	T=0.71
Siberian	Global	Study-wide	46	C=0.26	T=0.74
The Danish reference pan genome	Danish	Study-wide	40	C=0.45	T=0.55

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.48895503C>A
GRCh38.p14 chr 17	NC_000017.11:g.48895503C>T
GRCh37.p13 chr 17	NC_000017.10:g.46972865C>A
GRCh37.p13 chr 17	NC_000017.10:g.46972865C>T

Gene: ATP5MC1, ATP synthase membrane subunit c locus 1 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
ATP5MC1 transcript variant 2	NM_001002027.2:c.297-152C… NM_001002027.2:c.297-152C>A	N/A	Intron Variant
ATP5MC1 transcript variant 1	NM_005175.3:c.297-152C>A	N/A	Intron 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	C=	A	T
GRCh38.p14 chr 17	NC_000017.11:g.48895503=	NC_000017.11:g.48895503C>A	NC_000017.11:g.48895503C>T
GRCh37.p13 chr 17	NC_000017.10:g.46972865=	NC_000017.10:g.46972865C>A	NC_000017.10:g.46972865C>T
ATP5MC1 transcript variant 2	NM_001002027.1:c.297-152=	NM_001002027.1:c.297-152C>A	NM_001002027.1:c.297-152C>T
ATP5MC1 transcript variant 2	NM_001002027.2:c.297-152=	NM_001002027.2:c.297-152C>A	NM_001002027.2:c.297-152C>T
ATP5MC1 transcript variant 1	NM_005175.2:c.297-152=	NM_005175.2:c.297-152C>A	NM_005175.2:c.297-152C>T
ATP5MC1 transcript variant 1	NM_005175.3:c.297-152=	NM_005175.3:c.297-152C>A	NM_005175.3:c.297-152C>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#.

72 SubSNP, 21 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	KWOK	ss1145465	Oct 05, 2000 (86)
2	KWOK	ss1912465	Oct 18, 2000 (87)
3	SC_JCM	ss3724710	Sep 28, 2001 (100)
4	CSHL-HAPMAP	ss20034998	Feb 27, 2004 (120)
5	ABI	ss44050483	Mar 14, 2006 (126)
6	BCMHGSC_JDW	ss90605683	Mar 24, 2008 (129)
7	BGI	ss106509324	Feb 05, 2009 (130)
8	ENSEMBL	ss137096858	Dec 01, 2009 (131)
9	GMI	ss158067664	Dec 01, 2009 (131)
10	ENSEMBL	ss161832535	Dec 01, 2009 (131)
11	BUSHMAN	ss202567147	Jul 04, 2010 (132)
12	1000GENOMES	ss237257878	Jul 15, 2010 (132)
13	1000GENOMES	ss243550799	Jul 15, 2010 (132)
14	BL	ss255663510	May 09, 2011 (134)
15	GMI	ss282779191	May 04, 2012 (137)
16	GMI	ss287186356	Apr 25, 2013 (138)
17	PJP	ss292059601	May 09, 2011 (134)
18	TISHKOFF	ss565294737	Apr 25, 2013 (138)
19	SSMP	ss661102278	Apr 25, 2013 (138)
20	EVA-GONL	ss993148606	Aug 21, 2014 (142)
21	JMKIDD_LAB	ss1081084332	Aug 21, 2014 (142)
22	1000GENOMES	ss1358813518	Aug 21, 2014 (142)
23	DDI	ss1428043436	Apr 01, 2015 (144)
24	EVA_GENOME_DK	ss1578173698	Apr 01, 2015 (144)
25	EVA_UK10K_ALSPAC	ss1635727723	Apr 01, 2015 (144)
26	EVA_UK10K_TWINSUK	ss1678721756	Apr 01, 2015 (144)
27	EVA_DECODE	ss1697191536	Apr 01, 2015 (144)
28	EVA_MGP	ss1711464749	Apr 01, 2015 (144)
29	WEILL_CORNELL_DGM	ss1936610834	Feb 12, 2016 (147)
30	GENOMED	ss1968397376	Jul 19, 2016 (147)
31	JJLAB	ss2029081647	Sep 14, 2016 (149)
32	USC_VALOUEV	ss2157556698	Dec 20, 2016 (150)
33	HUMAN_LONGEVITY	ss2217144222	Dec 20, 2016 (150)
34	SYSTEMSBIOZJU	ss2629036287	Nov 08, 2017 (151)
35	GRF	ss2702116545	Nov 08, 2017 (151)
36	GNOMAD	ss2950362634	Nov 08, 2017 (151)
37	SWEGEN	ss3015607698	Nov 08, 2017 (151)
38	BIOINF_KMB_FNS_UNIBA	ss3028362490	Nov 08, 2017 (151)
39	CSHL	ss3351761943	Nov 08, 2017 (151)
40	EGCUT_WGS	ss3682481402	Jul 13, 2019 (153)
41	EVA_DECODE	ss3700549747	Jul 13, 2019 (153)
42	ACPOP	ss3742061781	Jul 13, 2019 (153)
43	EVA	ss3754715248	Jul 13, 2019 (153)
44	PACBIO	ss3788218897	Jul 13, 2019 (153)
45	PACBIO	ss3793173782	Jul 13, 2019 (153)
46	PACBIO	ss3798059542	Jul 13, 2019 (153)
47	KHV_HUMAN_GENOMES	ss3819982425	Jul 13, 2019 (153)
48	EVA	ss3834889001	Apr 27, 2020 (154)
49	EVA	ss3841056716	Apr 27, 2020 (154)
50	EVA	ss3846553696	Apr 27, 2020 (154)
51	SGDP_PRJ	ss3885837432	Apr 27, 2020 (154)
52	KRGDB	ss3935547936	Apr 27, 2020 (154)
53	KOGIC	ss3978920857	Apr 27, 2020 (154)
54	FSA-LAB	ss3984118081	Apr 26, 2021 (155)
55	EVA	ss3985793063	Apr 26, 2021 (155)
56	TOPMED	ss5037404915	Apr 26, 2021 (155)
57	TOMMO_GENOMICS	ss5222626406	Apr 26, 2021 (155)
58	1000G_HIGH_COVERAGE	ss5303280451	Oct 16, 2022 (156)
59	EVA	ss5427851690	Oct 16, 2022 (156)
60	HUGCELL_USP	ss5496312921	Oct 16, 2022 (156)
61	EVA	ss5511779771	Oct 16, 2022 (156)
62	1000G_HIGH_COVERAGE	ss5607069905	Oct 16, 2022 (156)
63	SANFORD_IMAGENETICS	ss5660184225	Oct 16, 2022 (156)
64	TOMMO_GENOMICS	ss5778904315	Oct 16, 2022 (156)
65	EVA	ss5800209668	Oct 16, 2022 (156)
66	YY_MCH	ss5816576117	Oct 16, 2022 (156)
67	EVA	ss5834041987	Oct 16, 2022 (156)
68	EVA	ss5851822516	Oct 16, 2022 (156)
69	EVA	ss5914092033	Oct 16, 2022 (156)
70	EVA	ss5936568181	Oct 16, 2022 (156)
71	EVA	ss5951572801	Oct 16, 2022 (156)
72	EVA	ss5980970950	Oct 16, 2022 (156)
73	1000Genomes	NC_000017.10 - 46972865	Oct 12, 2018 (152)
74	1000Genomes_30x	NC_000017.11 - 48895503	Oct 16, 2022 (156)
75	The Avon Longitudinal Study of Parents and Children	NC_000017.10 - 46972865	Oct 12, 2018 (152)
76	Genetic variation in the Estonian population	NC_000017.10 - 46972865	Oct 12, 2018 (152)
77	The Danish reference pan genome	NC_000017.10 - 46972865	Apr 27, 2020 (154)
78	gnomAD - Genomes	NC_000017.11 - 48895503	Apr 26, 2021 (155)
79	Genome of the Netherlands Release 5	NC_000017.10 - 46972865	Apr 27, 2020 (154)
80	KOREAN population from KRGDB	NC_000017.10 - 46972865	Apr 27, 2020 (154)
81	Korean Genome Project	NC_000017.11 - 48895503	Apr 27, 2020 (154)
82	Medical Genome Project healthy controls from Spanish population	NC_000017.10 - 46972865	Apr 27, 2020 (154)
83	Northern Sweden	NC_000017.10 - 46972865	Jul 13, 2019 (153)
84	Ancient Sardinia genome-wide 1240k capture data generation and analysis	NC_000017.10 - 46972865	Apr 26, 2021 (155)
85	Qatari	NC_000017.10 - 46972865	Apr 27, 2020 (154)
86	SGDP_PRJ	NC_000017.10 - 46972865	Apr 27, 2020 (154)
87	Siberian	NC_000017.10 - 46972865	Apr 27, 2020 (154)
88	8.3KJPN	NC_000017.10 - 46972865	Apr 26, 2021 (155)
89	14KJPN	NC_000017.11 - 48895503	Oct 16, 2022 (156)
90	TopMed	NC_000017.11 - 48895503	Apr 26, 2021 (155)
91	UK 10K study - Twins	NC_000017.10 - 46972865	Oct 12, 2018 (152)
92	A Vietnamese Genetic Variation Database	NC_000017.10 - 46972865	Jul 13, 2019 (153)
93	ALFA	NC_000017.11 - 48895503	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
42725330, ss3935547936	NC_000017.10:46972864:C:A	NC_000017.11:48895502:C:A	(self)
ss90605683, ss202567147, ss255663510, ss282779191, ss287186356, ss292059601, ss1697191536	NC_000017.9:44327863:C:T	NC_000017.11:48895502:C:T	(self)
72061515, 39933031, 28219650, 4375356, 17798117, 42725330, 580509, 15346646, 1018990, 18652756, 37854412, 10073052, 80595713, 39933031, 8833844, ss237257878, ss243550799, ss565294737, ss661102278, ss993148606, ss1081084332, ss1358813518, ss1428043436, ss1578173698, ss1635727723, ss1678721756, ss1711464749, ss1936610834, ss1968397376, ss2029081647, ss2157556698, ss2629036287, ss2702116545, ss2950362634, ss3015607698, ss3351761943, ss3682481402, ss3742061781, ss3754715248, ss3788218897, ss3793173782, ss3798059542, ss3834889001, ss3841056716, ss3885837432, ss3935547936, ss3984118081, ss3985793063, ss5222626406, ss5427851690, ss5511779771, ss5660184225, ss5800209668, ss5834041987, ss5936568181, ss5951572801, ss5980970950	NC_000017.10:46972864:C:T	NC_000017.11:48895502:C:T	(self)
94595840, 508487207, 35298858, 112741419, 252950577, 3879253832, ss2217144222, ss3028362490, ss3700549747, ss3819982425, ss3846553696, ss3978920857, ss5037404915, ss5303280451, ss5496312921, ss5607069905, ss5778904315, ss5816576117, ss5851822516, ss5914092033	NC_000017.11:48895502:C:T	NC_000017.11:48895502:C:T	(self)
ss20034998	NT_010783.14:5626142:C:T	NC_000017.11:48895502:C:T	(self)
ss1145465, ss1912465, ss3724710, ss44050483, ss106509324, ss137096858, ss158067664, ss161832535	NT_010783.15:12247016:C:T	NC_000017.11:48895502:C: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 rs832410

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

rs832410