Name: rs146174090
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.

rs146174090

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr2:175178321 (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>T
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.000136 (36/264690, TOPMED)
T=0.000694 (172/247832, GnomAD_exome)
T=0.000378 (53/140200, GnomAD) (+ 11 more)
T=0.000745 (90/120770, ExAC)
T=0.00030 (12/40268, ALFA)
T=0.00023 (3/13006, GO-ESP)
T=0.0002 (1/6404, 1000G_30x)
T=0.0002 (1/5008, 1000G)
T=0.0009 (4/4480, Estonian)
T=0.0007 (2/2922, KOREAN)
T=0.007 (4/600, NorthernSweden)
T=0.007 (2/304, FINRISK)
C=0.5 (1/2, SGDP_PRJ)
T=0.5 (1/2, SGDP_PRJ)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: ATP5MC3 : Synonymous 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	56630	C=0.99968	T=0.00032
European	Sub	41274	C=0.99959	T=0.00041
African	Sub	7804	C=1.0000	T=0.0000
African Others	Sub	298	C=1.000	T=0.000
African American	Sub	7506	C=1.0000	T=0.0000
Asian	Sub	112	C=1.000	T=0.000
East Asian	Sub	86	C=1.00	T=0.00
Other Asian	Sub	26	C=1.00	T=0.00
Latin American 1	Sub	500	C=1.000	T=0.000
Latin American 2	Sub	628	C=1.000	T=0.000
South Asian	Sub	98	C=1.00	T=0.00
Other	Sub	6214	C=0.9998	T=0.0002

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	C=0.999864	T=0.000136
gnomAD - Exomes	Global	Study-wide	247832	C=0.999306	T=0.000694
gnomAD - Exomes	European	Sub	134248	C=0.998808	T=0.001192
gnomAD - Exomes	Asian	Sub	47646	C=0.99994	T=0.00006
gnomAD - Exomes	American	Sub	33782	C=1.00000	T=0.00000
gnomAD - Exomes	African	Sub	16154	C=1.00000	T=0.00000
gnomAD - Exomes	Ashkenazi Jewish	Sub	9946	C=1.0000	T=0.0000
gnomAD - Exomes	Other	Sub	6056	C=0.9985	T=0.0015
gnomAD - Genomes	Global	Study-wide	140200	C=0.999622	T=0.000378
gnomAD - Genomes	European	Sub	75920	C=0.99930	T=0.00070
gnomAD - Genomes	African	Sub	42018	C=1.00000	T=0.00000
gnomAD - Genomes	American	Sub	13658	C=1.00000	T=0.00000
gnomAD - Genomes	Ashkenazi Jewish	Sub	3320	C=1.0000	T=0.0000
gnomAD - Genomes	East Asian	Sub	3134	C=1.0000	T=0.0000
gnomAD - Genomes	Other	Sub	2150	C=1.0000	T=0.0000
ExAC	Global	Study-wide	120770	C=0.999255	T=0.000745
ExAC	Europe	Sub	72980	C=0.99882	T=0.00118
ExAC	Asian	Sub	25094	C=0.99996	T=0.00004
ExAC	American	Sub	11536	C=1.00000	T=0.00000
ExAC	African	Sub	10260	C=1.00000	T=0.00000
ExAC	Other	Sub	900	C=0.997	T=0.003
Allele Frequency Aggregator	Total	Global	40268	C=0.99970	T=0.00030
Allele Frequency Aggregator	European	Sub	31184	C=0.99965	T=0.00035
Allele Frequency Aggregator	Other	Sub	4780	C=0.9998	T=0.0002
Allele Frequency Aggregator	African	Sub	2966	C=1.0000	T=0.0000
Allele Frequency Aggregator	Latin American 2	Sub	628	C=1.000	T=0.000
Allele Frequency Aggregator	Latin American 1	Sub	500	C=1.000	T=0.000
Allele Frequency Aggregator	Asian	Sub	112	C=1.000	T=0.000
Allele Frequency Aggregator	South Asian	Sub	98	C=1.00	T=0.00
GO Exome Sequencing Project	Global	Study-wide	13006	C=0.99977	T=0.00023
GO Exome Sequencing Project	European American	Sub	8600	C=0.9997	T=0.0003
GO Exome Sequencing Project	African American	Sub	4406	C=1.0000	T=0.0000
1000Genomes_30x	Global	Study-wide	6404	C=0.9998	T=0.0002
1000Genomes_30x	African	Sub	1786	C=1.0000	T=0.0000
1000Genomes_30x	Europe	Sub	1266	C=0.9992	T=0.0008
1000Genomes_30x	South Asian	Sub	1202	C=1.0000	T=0.0000
1000Genomes_30x	East Asian	Sub	1170	C=1.0000	T=0.0000
1000Genomes_30x	American	Sub	980	C=1.000	T=0.000
1000Genomes	Global	Study-wide	5008	C=0.9998	T=0.0002
1000Genomes	African	Sub	1322	C=1.0000	T=0.0000
1000Genomes	East Asian	Sub	1008	C=1.0000	T=0.0000
1000Genomes	Europe	Sub	1006	C=0.9990	T=0.0010
1000Genomes	South Asian	Sub	978	C=1.000	T=0.000
1000Genomes	American	Sub	694	C=1.000	T=0.000
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.9991	T=0.0009
KOREAN population from KRGDB	KOREAN	Study-wide	2922	C=0.9993	T=0.0007
Northern Sweden	ACPOP	Study-wide	600	C=0.993	T=0.007
FINRISK	Finnish from FINRISK project	Study-wide	304	C=0.993	T=0.007
SGDP_PRJ	Global	Study-wide	2	C=0.5	T=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 2	NC_000002.12:g.175178321C>T
GRCh37.p13 chr 2	NC_000002.11:g.176043049C>T

Gene: ATP5MC3, ATP synthase membrane subunit c locus 3 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
ATP5MC3 transcript variant 4	NM_001190329.2:c.*732=	N/A	3 Prime UTR Variant
ATP5MC3 transcript variant 3	NM_001002258.5:c.396G>A	L [TTG] > L [TTA]	Coding Sequence Variant
ATP synthase F(0) complex subunit C3, mitochondrial isoform A precursor	NP_001002258.1:p.Leu132=	L (Leu) > L (Leu)	Synonymous Variant
ATP5MC3 transcript variant 2	NM_001689.5:c.396G>A	L [TTG] > L [TTA]	Coding Sequence Variant
ATP synthase F(0) complex subunit C3, mitochondrial isoform A precursor	NP_001680.1:p.Leu132=	L (Leu) > L (Leu)	Synonymous 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=	T
GRCh38.p14 chr 2	NC_000002.12:g.175178321=	NC_000002.12:g.175178321C>T
GRCh37.p13 chr 2	NC_000002.11:g.176043049=	NC_000002.11:g.176043049C>T
ATP5MC3 transcript variant 3	NM_001002258.5:c.396=	NM_001002258.5:c.396G>A
ATP5MC3 transcript variant 3	NM_001002258.4:c.396=	NM_001002258.4:c.396G>A
ATP5MC3 transcript variant 2	NM_001689.5:c.396=	NM_001689.5:c.396G>A
ATP5MC3 transcript variant 2	NM_001689.4:c.396=	NM_001689.4:c.396G>A
ATP5MC3 transcript variant 4	NM_001190329.2:c.*732=	NM_001190329.2:c.*732G>A
ATP5MC3 transcript variant 4	NM_001190329.1:c.*732=	NM_001190329.1:c.*732G>A
ATP5G3 transcript variant 1	NM_001002256.1:c.396=	NM_001002256.1:c.396G>A
ATP synthase F(0) complex subunit C3, mitochondrial isoform A precursor	NP_001002258.1:p.Leu132=	NP_001002258.1:p.Leu132=
ATP synthase F(0) complex subunit C3, mitochondrial isoform A precursor	NP_001680.1:p.Leu132=	NP_001680.1:p.Leu132=

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#.

23 SubSNP, 13 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	NHLBI-ESP	ss342087400	May 09, 2011 (134)
2	1000GENOMES	ss455636633	Sep 17, 2011 (135)
3	1000GENOMES	ss489842033	May 04, 2012 (137)
4	CLINSEQ_SNP	ss491795062	May 04, 2012 (137)
5	1000GENOMES	ss1300527618	Aug 21, 2014 (142)
6	EVA_FINRISK	ss1584022159	Apr 01, 2015 (144)
7	EVA_DECODE	ss1587111418	Apr 01, 2015 (144)
8	EVA_EXAC	ss1686605499	Apr 01, 2015 (144)
9	GNOMAD	ss2733128568	Nov 08, 2017 (151)
10	GNOMAD	ss2746820710	Nov 08, 2017 (151)
11	GNOMAD	ss2783105628	Nov 08, 2017 (151)
12	SWEGEN	ss2990907361	Nov 08, 2017 (151)
13	EGCUT_WGS	ss3658780677	Jul 13, 2019 (153)
14	EVA_DECODE	ss3705476881	Jul 13, 2019 (153)
15	ACPOP	ss3729130681	Jul 13, 2019 (153)
16	EVA	ss3757752162	Jul 13, 2019 (153)
17	EVA	ss3823828313	Apr 25, 2020 (154)
18	SGDP_PRJ	ss3854028311	Apr 25, 2020 (154)
19	KRGDB	ss3899671386	Apr 25, 2020 (154)
20	TOPMED	ss4534615860	Apr 26, 2021 (155)
21	EVA	ss5334256218	Oct 12, 2022 (156)
22	1000G_HIGH_COVERAGE	ss5527885683	Oct 12, 2022 (156)
23	EVA	ss5933581773	Oct 12, 2022 (156)
24	1000Genomes	NC_000002.11 - 176043049	Oct 11, 2018 (152)
25	1000Genomes_30x	NC_000002.12 - 175178321	Oct 12, 2022 (156)
26	Genetic variation in the Estonian population	NC_000002.11 - 176043049	Oct 11, 2018 (152)
27	ExAC	NC_000002.11 - 176043049	Oct 11, 2018 (152)
28	FINRISK	NC_000002.11 - 176043049	Apr 25, 2020 (154)
29	gnomAD - Genomes	NC_000002.12 - 175178321	Apr 26, 2021 (155)
30	gnomAD - Exomes	NC_000002.11 - 176043049	Jul 13, 2019 (153)
31	GO Exome Sequencing Project	NC_000002.11 - 176043049	Oct 11, 2018 (152)
32	KOREAN population from KRGDB	NC_000002.11 - 176043049	Apr 25, 2020 (154)
33	Northern Sweden	NC_000002.11 - 176043049	Jul 13, 2019 (153)
34	SGDP_PRJ	NC_000002.11 - 176043049	Apr 25, 2020 (154)
35	TopMed	NC_000002.12 - 175178321	Apr 26, 2021 (155)
36	ALFA	NC_000002.12 - 175178321	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
ss491795062, ss1587111418	NC_000002.10:175751294:C:T	NC_000002.12:175178320:C:T	(self)
11589305, 4518925, 6499735, 18620, 2188709, 286745, 6848780, 2415546, 6045291, ss342087400, ss455636633, ss489842033, ss1300527618, ss1584022159, ss1686605499, ss2733128568, ss2746820710, ss2783105628, ss2990907361, ss3658780677, ss3729130681, ss3757752162, ss3823828313, ss3854028311, ss3899671386, ss5334256218	NC_000002.11:176043048:C:T	NC_000002.12:175178320:C:T	(self)
15411618, 82611253, 338438739, 2146179352, ss3705476881, ss4534615860, ss5527885683, ss5933581773	NC_000002.12:175178320:C:T	NC_000002.12:175178320: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 rs146174090

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

rs146174090