Name: rs3789491
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.

rs3789491

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:6316162 (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>C
Variation Type: SNV Single Nucleotide Variation
Frequency: C=0.095580 (25299/264690, TOPMED)
C=0.088148 (12359/140208, GnomAD)
C=0.14102 (3985/28258, 14KJPN) (+ 18 more)
C=0.06834 (1664/24350, ALFA)
C=0.14147 (2371/16760, 8.3KJPN)
C=0.1063 (681/6404, 1000G_30x)
C=0.1040 (521/5008, 1000G)
C=0.0259 (116/4480, Estonian)
C=0.0376 (145/3854, ALSPAC)
C=0.0380 (141/3708, TWINSUK)
C=0.1314 (385/2930, KOREAN)
C=0.1617 (306/1892, HapMap)
C=0.1392 (255/1832, Korea1K)
C=0.036 (36/998, GoNL)
C=0.033 (20/600, NorthernSweden)
C=0.190 (41/216, Qatari)
C=0.085 (18/212, Vietnamese)
T=0.46 (43/94, SGDP_PRJ)
C=0.03 (1/40, GENOME_DK)
T=0.5 (2/4, Siberian)
C=0.5 (2/4, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: ACOT7 : 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	24350	T=0.93166	C=0.06834
European	Sub	18126	T=0.96188	C=0.03812
African	Sub	4114	T=0.7990	C=0.2010
African Others	Sub	148	T=0.743	C=0.257
African American	Sub	3966	T=0.8011	C=0.1989
Asian	Sub	124	T=0.871	C=0.129
East Asian	Sub	96	T=0.88	C=0.12
Other Asian	Sub	28	T=0.86	C=0.14
Latin American 1	Sub	168	T=0.893	C=0.107
Latin American 2	Sub	670	T=0.940	C=0.060
South Asian	Sub	98	T=0.98	C=0.02
Other	Sub	1050	T=0.9333	C=0.0667

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=0.904420	C=0.095580
gnomAD - Genomes	Global	Study-wide	140208	T=0.911852	C=0.088148
gnomAD - Genomes	European	Sub	75952	T=0.96550	C=0.03450
gnomAD - Genomes	African	Sub	41992	T=0.81058	C=0.18942
gnomAD - Genomes	American	Sub	13656	T=0.93710	C=0.06290
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	T=0.8845	C=0.1155
gnomAD - Genomes	East Asian	Sub	3132	T=0.8838	C=0.1162
gnomAD - Genomes	Other	Sub	2152	T=0.9173	C=0.0827
14KJPN	JAPANESE	Study-wide	28258	T=0.85898	C=0.14102
Allele Frequency Aggregator	Total	Global	24350	T=0.93166	C=0.06834
Allele Frequency Aggregator	European	Sub	18126	T=0.96188	C=0.03812
Allele Frequency Aggregator	African	Sub	4114	T=0.7990	C=0.2010
Allele Frequency Aggregator	Other	Sub	1050	T=0.9333	C=0.0667
Allele Frequency Aggregator	Latin American 2	Sub	670	T=0.940	C=0.060
Allele Frequency Aggregator	Latin American 1	Sub	168	T=0.893	C=0.107
Allele Frequency Aggregator	Asian	Sub	124	T=0.871	C=0.129
Allele Frequency Aggregator	South Asian	Sub	98	T=0.98	C=0.02
8.3KJPN	JAPANESE	Study-wide	16760	T=0.85853	C=0.14147
1000Genomes_30x	Global	Study-wide	6404	T=0.8937	C=0.1063
1000Genomes_30x	African	Sub	1786	T=0.7861	C=0.2139
1000Genomes_30x	Europe	Sub	1266	T=0.9637	C=0.0363
1000Genomes_30x	South Asian	Sub	1202	T=0.9443	C=0.0557
1000Genomes_30x	East Asian	Sub	1170	T=0.8803	C=0.1197
1000Genomes_30x	American	Sub	980	T=0.953	C=0.047
1000Genomes	Global	Study-wide	5008	T=0.8960	C=0.1040
1000Genomes	African	Sub	1322	T=0.7874	C=0.2126
1000Genomes	East Asian	Sub	1008	T=0.8819	C=0.1181
1000Genomes	Europe	Sub	1006	T=0.9662	C=0.0338
1000Genomes	South Asian	Sub	978	T=0.945	C=0.055
1000Genomes	American	Sub	694	T=0.952	C=0.048
Genetic variation in the Estonian population	Estonian	Study-wide	4480	T=0.9741	C=0.0259
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.9624	C=0.0376
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.9620	C=0.0380
KOREAN population from KRGDB	KOREAN	Study-wide	2930	T=0.8686	C=0.1314
HapMap	Global	Study-wide	1892	T=0.8383	C=0.1617
HapMap	American	Sub	770	T=0.919	C=0.081
HapMap	African	Sub	692	T=0.727	C=0.273
HapMap	Asian	Sub	254	T=0.827	C=0.173
HapMap	Europe	Sub	176	T=0.938	C=0.062
Korean Genome Project	KOREAN	Study-wide	1832	T=0.8608	C=0.1392
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.964	C=0.036
Northern Sweden	ACPOP	Study-wide	600	T=0.967	C=0.033
Qatari	Global	Study-wide	216	T=0.810	C=0.190
A Vietnamese Genetic Variation Database	Global	Study-wide	212	T=0.915	C=0.085
SGDP_PRJ	Global	Study-wide	94	T=0.46	C=0.54
The Danish reference pan genome	Danish	Study-wide	40	T=0.97	C=0.03
Siberian	Global	Study-wide	4	T=0.5	C=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 1	NC_000001.11:g.6316162T>C
GRCh37.p13 chr 1	NC_000001.10:g.6376222T>C

Gene: ACOT7, acyl-CoA thioesterase 7 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
ACOT7 transcript variant hBACHa	NM_007274.4:c.712+2330A>G	N/A	Intron Variant
ACOT7 transcript variant hBACHb	NM_181864.3:c.742+2330A>G	N/A	Intron Variant
ACOT7 transcript variant hBACHc	NM_181865.3:c.652+2330A>G	N/A	Intron Variant
ACOT7 transcript variant hBACHd	NM_181866.3:c.589+2330A>G	N/A	Intron Variant
ACOT7 transcript variant X1	XM_047443399.1:c.565+2330… XM_047443399.1:c.565+2330A>G	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=	C
GRCh38.p14 chr 1	NC_000001.11:g.6316162=	NC_000001.11:g.6316162T>C
GRCh37.p13 chr 1	NC_000001.10:g.6376222=	NC_000001.10:g.6376222T>C
ACOT7 transcript variant hBACHa	NM_007274.3:c.712+2330=	NM_007274.3:c.712+2330A>G
ACOT7 transcript variant hBACHa	NM_007274.4:c.712+2330=	NM_007274.4:c.712+2330A>G
ACOT7 transcript variant hBACHb	NM_181864.2:c.742+2330=	NM_181864.2:c.742+2330A>G
ACOT7 transcript variant hBACHb	NM_181864.3:c.742+2330=	NM_181864.3:c.742+2330A>G
ACOT7 transcript variant hBACHc	NM_181865.2:c.652+2330=	NM_181865.2:c.652+2330A>G
ACOT7 transcript variant hBACHc	NM_181865.3:c.652+2330=	NM_181865.3:c.652+2330A>G
ACOT7 transcript variant hBACHd	NM_181866.2:c.589+2330=	NM_181866.2:c.589+2330A>G
ACOT7 transcript variant hBACHd	NM_181866.3:c.589+2330=	NM_181866.3:c.589+2330A>G
ACOT7 transcript variant X1	XM_005263427.1:c.652+2330=	XM_005263427.1:c.652+2330A>G
ACOT7 transcript variant X1	XM_047443399.1:c.565+2330=	XM_047443399.1:c.565+2330A>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#.

67 SubSNP, 20 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	YUSUKE	ss4975861	Aug 28, 2002 (107)
2	ILLUMINA	ss65786942	Oct 15, 2006 (127)
3	AFFY	ss65978933	Nov 30, 2006 (127)
4	ILLUMINA	ss74988707	Dec 07, 2007 (129)
5	HGSV	ss81325805	Dec 14, 2007 (130)
6	HGSV	ss84966044	Dec 14, 2007 (130)
7	1000GENOMES	ss110003701	Jan 24, 2009 (130)
8	ILLUMINA-UK	ss118472135	Feb 14, 2009 (130)
9	KRIBB_YJKIM	ss119462915	Dec 01, 2009 (131)
10	ENSEMBL	ss137777973	Dec 01, 2009 (131)
11	GMI	ss154592002	Dec 01, 2009 (131)
12	COMPLETE_GENOMICS	ss163030912	Jul 04, 2010 (132)
13	ILLUMINA	ss173640180	Jul 04, 2010 (132)
14	BUSHMAN	ss197963675	Jul 04, 2010 (132)
15	1000GENOMES	ss218217492	Jul 14, 2010 (132)
16	1000GENOMES	ss230414100	Jul 14, 2010 (132)
17	1000GENOMES	ss238131358	Jul 15, 2010 (132)
18	GMI	ss275700822	May 04, 2012 (137)
19	PJP	ss290569320	May 09, 2011 (134)
20	ILLUMINA	ss537194649	Sep 08, 2015 (146)
21	TISHKOFF	ss553755976	Apr 25, 2013 (138)
22	SSMP	ss647552133	Apr 25, 2013 (138)
23	EVA-GONL	ss974819461	Aug 21, 2014 (142)
24	JMKIDD_LAB	ss1067644777	Aug 21, 2014 (142)
25	1000GENOMES	ss1289538086	Aug 21, 2014 (142)
26	DDI	ss1425701378	Apr 01, 2015 (144)
27	EVA_GENOME_DK	ss1573870103	Apr 01, 2015 (144)
28	EVA_DECODE	ss1584177671	Apr 01, 2015 (144)
29	EVA_UK10K_ALSPAC	ss1599473730	Apr 01, 2015 (144)
30	EVA_UK10K_TWINSUK	ss1642467763	Apr 01, 2015 (144)
31	EVA_SVP	ss1712308731	Apr 01, 2015 (144)
32	WEILL_CORNELL_DGM	ss1918016943	Feb 12, 2016 (147)
33	JJLAB	ss2019524294	Sep 14, 2016 (149)
34	USC_VALOUEV	ss2147517404	Dec 20, 2016 (150)
35	HUMAN_LONGEVITY	ss2159747279	Dec 20, 2016 (150)
36	SYSTEMSBIOZJU	ss2624278098	Nov 08, 2017 (151)
37	GRF	ss2697412951	Nov 08, 2017 (151)
38	GNOMAD	ss2751202585	Nov 08, 2017 (151)
39	SWEGEN	ss2986236814	Nov 08, 2017 (151)
40	CSHL	ss3343301384	Nov 08, 2017 (151)
41	ILLUMINA	ss3626017670	Oct 11, 2018 (152)
42	ILLUMINA	ss3637735133	Oct 11, 2018 (152)
43	ILLUMINA	ss3642749198	Oct 11, 2018 (152)
44	EGCUT_WGS	ss3654337294	Jul 12, 2019 (153)
45	EVA_DECODE	ss3686090339	Jul 12, 2019 (153)
46	ACPOP	ss3726759548	Jul 12, 2019 (153)
47	EVA	ss3745784837	Jul 12, 2019 (153)
48	KHV_HUMAN_GENOMES	ss3798805312	Jul 12, 2019 (153)
49	EVA	ss3826006111	Apr 25, 2020 (154)
50	SGDP_PRJ	ss3848117887	Apr 25, 2020 (154)
51	KRGDB	ss3892984801	Apr 25, 2020 (154)
52	KOGIC	ss3943739990	Apr 25, 2020 (154)
53	EVA	ss4016891432	Apr 25, 2021 (155)
54	TOPMED	ss4437984123	Apr 25, 2021 (155)
55	TOMMO_GENOMICS	ss5142298199	Apr 25, 2021 (155)
56	1000G_HIGH_COVERAGE	ss5241043823	Oct 17, 2022 (156)
57	EVA	ss5316513779	Oct 17, 2022 (156)
58	HUGCELL_USP	ss5442261292	Oct 17, 2022 (156)
59	EVA	ss5505757327	Oct 17, 2022 (156)
60	1000G_HIGH_COVERAGE	ss5512743851	Oct 17, 2022 (156)
61	SANFORD_IMAGENETICS	ss5624852825	Oct 17, 2022 (156)
62	TOMMO_GENOMICS	ss5666542795	Oct 17, 2022 (156)
63	YY_MCH	ss5800291352	Oct 17, 2022 (156)
64	EVA	ss5831490700	Oct 17, 2022 (156)
65	EVA	ss5848769146	Oct 17, 2022 (156)
66	EVA	ss5906898103	Oct 17, 2022 (156)
67	EVA	ss5936679050	Oct 17, 2022 (156)
68	1000Genomes	NC_000001.10 - 6376222	Oct 11, 2018 (152)
69	1000Genomes_30x	NC_000001.11 - 6316162	Oct 17, 2022 (156)
70	The Avon Longitudinal Study of Parents and Children	NC_000001.10 - 6376222	Oct 11, 2018 (152)
71	Genetic variation in the Estonian population	NC_000001.10 - 6376222	Oct 11, 2018 (152)
72	The Danish reference pan genome	NC_000001.10 - 6376222	Apr 25, 2020 (154)
73	gnomAD - Genomes	NC_000001.11 - 6316162	Apr 25, 2021 (155)
74	Genome of the Netherlands Release 5	NC_000001.10 - 6376222	Apr 25, 2020 (154)
75	HapMap	NC_000001.11 - 6316162	Apr 25, 2020 (154)
76	KOREAN population from KRGDB	NC_000001.10 - 6376222	Apr 25, 2020 (154)
77	Korean Genome Project	NC_000001.11 - 6316162	Apr 25, 2020 (154)
78	Northern Sweden	NC_000001.10 - 6376222	Jul 12, 2019 (153)
79	Qatari	NC_000001.10 - 6376222	Apr 25, 2020 (154)
80	SGDP_PRJ	NC_000001.10 - 6376222	Apr 25, 2020 (154)
81	Siberian	NC_000001.10 - 6376222	Apr 25, 2020 (154)
82	8.3KJPN	NC_000001.10 - 6376222	Apr 25, 2021 (155)
83	14KJPN	NC_000001.11 - 6316162	Oct 17, 2022 (156)
84	TopMed	NC_000001.11 - 6316162	Apr 25, 2021 (155)
85	UK 10K study - Twins	NC_000001.10 - 6376222	Oct 11, 2018 (152)
86	A Vietnamese Genetic Variation Database	NC_000001.10 - 6376222	Jul 12, 2019 (153)
87	ALFA	NC_000001.11 - 6316162	Apr 25, 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)
rs58000799	May 24, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss81325805, ss84966044	NC_000001.8:6310487:T:C	NC_000001.11:6316161:T:C	(self)
ss110003701, ss118472135, ss163030912, ss197963675, ss275700822, ss290569320, ss1584177671, ss1712308731, ss3642749198	NC_000001.9:6298808:T:C	NC_000001.11:6316161:T:C	(self)
208757, 103913, 75542, 1376862, 45289, 162195, 44413, 58873, 134867, 33758, 267506, 103913, 22927, ss218217492, ss230414100, ss238131358, ss537194649, ss553755976, ss647552133, ss974819461, ss1067644777, ss1289538086, ss1425701378, ss1573870103, ss1599473730, ss1642467763, ss1918016943, ss2019524294, ss2147517404, ss2624278098, ss2697412951, ss2751202585, ss2986236814, ss3343301384, ss3626017670, ss3637735133, ss3654337294, ss3726759548, ss3745784837, ss3826006111, ss3848117887, ss3892984801, ss4016891432, ss5142298199, ss5316513779, ss5505757327, ss5624852825, ss5831490700, ss5936679050	NC_000001.10:6376221:T:C	NC_000001.11:6316161:T:C	(self)
269786, 1435778, 7677, 117991, 379899, 1590458, 1336311570, ss2159747279, ss3686090339, ss3798805312, ss3943739990, ss4437984123, ss5241043823, ss5442261292, ss5512743851, ss5666542795, ss5800291352, ss5848769146, ss5906898103	NC_000001.11:6316161:T:C	NC_000001.11:6316161:T:C	(self)
ss4975861, ss65786942, ss65978933, ss74988707, ss119462915, ss137777973, ss154592002, ss173640180	NT_021937.19:2380953:T:C	NC_000001.11:6316161:T:C	(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 rs3789491

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

rs3789491