Name: rs12954864
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.

rs12954864

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr18:59029656 (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: A>G
Variation Type: SNV Single Nucleotide Variation
Frequency: G=0.088447 (23411/264690, TOPMED)
G=0.085605 (11945/139536, GnomAD)
G=0.07264 (2242/30866, ALFA) (+ 17 more)
G=0.02477 (700/28258, 14KJPN)
G=0.02655 (445/16760, 8.3KJPN)
G=0.0870 (557/6404, 1000G_30x)
G=0.0845 (423/5008, 1000G)
G=0.0446 (200/4480, Estonian)
G=0.0620 (239/3854, ALSPAC)
G=0.0709 (263/3708, TWINSUK)
G=0.0205 (60/2920, KOREAN)
G=0.075 (75/998, GoNL)
G=0.068 (41/600, NorthernSweden)
G=0.100 (32/320, HapMap)
G=0.106 (23/216, Qatari)
G=0.014 (3/216, Vietnamese)
A=0.42 (39/92, SGDP_PRJ)
G=0.05 (2/40, GENOME_DK)
A=0.5 (4/8, Siberian)
G=0.5 (4/8, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: OACYLP : 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	30866	A=0.92736	G=0.07264
European	Sub	24736	A=0.93564	G=0.06436
African	Sub	3168	A=0.8658	G=0.1342
African Others	Sub	124	A=0.839	G=0.161
African American	Sub	3044	A=0.8670	G=0.1330
Asian	Sub	128	A=0.992	G=0.008
East Asian	Sub	100	A=0.99	G=0.01
Other Asian	Sub	28	A=1.00	G=0.00
Latin American 1	Sub	168	A=0.929	G=0.071
Latin American 2	Sub	700	A=0.957	G=0.043
South Asian	Sub	114	A=0.939	G=0.061
Other	Sub	1852	A=0.9055	G=0.0945

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	A=0.911553	G=0.088447
gnomAD - Genomes	Global	Study-wide	139536	A=0.914395	G=0.085605
gnomAD - Genomes	European	Sub	75602	A=0.93640	G=0.06360
gnomAD - Genomes	African	Sub	41776	A=0.86681	G=0.13319
gnomAD - Genomes	American	Sub	13594	A=0.93225	G=0.06775
gnomAD - Genomes	Ashkenazi Jewish	Sub	3308	A=0.8869	G=0.1131
gnomAD - Genomes	East Asian	Sub	3118	A=0.9689	G=0.0311
gnomAD - Genomes	Other	Sub	2138	A=0.9153	G=0.0847
Allele Frequency Aggregator	Total	Global	30866	A=0.92736	G=0.07264
Allele Frequency Aggregator	European	Sub	24736	A=0.93564	G=0.06436
Allele Frequency Aggregator	African	Sub	3168	A=0.8658	G=0.1342
Allele Frequency Aggregator	Other	Sub	1852	A=0.9055	G=0.0945
Allele Frequency Aggregator	Latin American 2	Sub	700	A=0.957	G=0.043
Allele Frequency Aggregator	Latin American 1	Sub	168	A=0.929	G=0.071
Allele Frequency Aggregator	Asian	Sub	128	A=0.992	G=0.008
Allele Frequency Aggregator	South Asian	Sub	114	A=0.939	G=0.061
14KJPN	JAPANESE	Study-wide	28258	A=0.97523	G=0.02477
8.3KJPN	JAPANESE	Study-wide	16760	A=0.97345	G=0.02655
1000Genomes_30x	Global	Study-wide	6404	A=0.9130	G=0.0870
1000Genomes_30x	African	Sub	1786	A=0.8494	G=0.1506
1000Genomes_30x	Europe	Sub	1266	A=0.9163	G=0.0837
1000Genomes_30x	South Asian	Sub	1202	A=0.9218	G=0.0782
1000Genomes_30x	East Asian	Sub	1170	A=0.9778	G=0.0222
1000Genomes_30x	American	Sub	980	A=0.937	G=0.063
1000Genomes	Global	Study-wide	5008	A=0.9155	G=0.0845
1000Genomes	African	Sub	1322	A=0.8533	G=0.1467
1000Genomes	East Asian	Sub	1008	A=0.9772	G=0.0228
1000Genomes	Europe	Sub	1006	A=0.9165	G=0.0835
1000Genomes	South Asian	Sub	978	A=0.920	G=0.080
1000Genomes	American	Sub	694	A=0.937	G=0.063
Genetic variation in the Estonian population	Estonian	Study-wide	4480	A=0.9554	G=0.0446
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.9380	G=0.0620
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.9291	G=0.0709
KOREAN population from KRGDB	KOREAN	Study-wide	2920	A=0.9795	G=0.0205
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	A=0.925	G=0.075
Northern Sweden	ACPOP	Study-wide	600	A=0.932	G=0.068
HapMap	Global	Study-wide	320	A=0.900	G=0.100
HapMap	American	Sub	118	A=0.932	G=0.068
HapMap	African	Sub	112	A=0.821	G=0.179
HapMap	Asian	Sub	90	A=0.96	G=0.04
Qatari	Global	Study-wide	216	A=0.894	G=0.106
A Vietnamese Genetic Variation Database	Global	Study-wide	216	A=0.986	G=0.014
SGDP_PRJ	Global	Study-wide	92	A=0.42	G=0.58
The Danish reference pan genome	Danish	Study-wide	40	A=0.95	G=0.05
Siberian	Global	Study-wide	8	A=0.5	G=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 18	NC_000018.10:g.59029656A>G
GRCh37.p13 chr 18	NC_000018.9:g.56696888A>G

Gene: OACYLP, O-acyltransferase like, pseudogene (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
OACYLP transcript	NR_024021.3: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	A=	G
GRCh38.p14 chr 18	NC_000018.10:g.59029656=	NC_000018.10:g.59029656A>G
GRCh37.p13 chr 18	NC_000018.9:g.56696888=	NC_000018.9:g.56696888A>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#.

65 SubSNP, 19 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SSAHASNP	ss21441772	Apr 05, 2004 (121)
2	ABI	ss44131143	Mar 15, 2006 (126)
3	HGSV	ss78464694	Dec 07, 2007 (129)
4	HGSV	ss84075136	Dec 15, 2007 (130)
5	BCMHGSC_JDW	ss90812050	Mar 24, 2008 (129)
6	ILLUMINA-UK	ss117898314	Feb 14, 2009 (130)
7	ENSEMBL	ss132696674	Dec 01, 2009 (131)
8	COMPLETE_GENOMICS	ss168334504	Jul 04, 2010 (132)
9	1000GENOMES	ss227902941	Jul 14, 2010 (132)
10	1000GENOMES	ss237498538	Jul 15, 2010 (132)
11	BL	ss255709603	May 09, 2011 (134)
12	PJP	ss292084082	May 09, 2011 (134)
13	ILLUMINA	ss483749491	May 04, 2012 (137)
14	ILLUMINA	ss484305830	May 04, 2012 (137)
15	ILLUMINA	ss536489844	Sep 08, 2015 (146)
16	TISHKOFF	ss565691494	Apr 25, 2013 (138)
17	SSMP	ss661527130	Apr 25, 2013 (138)
18	ILLUMINA	ss780604068	Sep 08, 2015 (146)
19	ILLUMINA	ss782599110	Sep 08, 2015 (146)
20	ILLUMINA	ss836097264	Sep 08, 2015 (146)
21	EVA-GONL	ss993813285	Aug 21, 2014 (142)
22	JMKIDD_LAB	ss1081562773	Aug 21, 2014 (142)
23	1000GENOMES	ss1361347974	Aug 21, 2014 (142)
24	DDI	ss1428243990	Apr 01, 2015 (144)
25	EVA_GENOME_DK	ss1578438599	Apr 01, 2015 (144)
26	EVA_UK10K_ALSPAC	ss1637052418	Apr 01, 2015 (144)
27	EVA_UK10K_TWINSUK	ss1680046451	Apr 01, 2015 (144)
28	EVA_DECODE	ss1697875138	Apr 01, 2015 (144)
29	HAMMER_LAB	ss1809086348	Sep 08, 2015 (146)
30	WEILL_CORNELL_DGM	ss1937280703	Feb 12, 2016 (147)
31	GENOMED	ss1968543332	Jul 19, 2016 (147)
32	JJLAB	ss2029410959	Sep 14, 2016 (149)
33	USC_VALOUEV	ss2157918318	Dec 20, 2016 (150)
34	HUMAN_LONGEVITY	ss2222245260	Dec 20, 2016 (150)
35	ILLUMINA	ss2633483159	Nov 08, 2017 (151)
36	GRF	ss2702509826	Nov 08, 2017 (151)
37	GNOMAD	ss2957598952	Nov 08, 2017 (151)
38	SWEGEN	ss3016658026	Nov 08, 2017 (151)
39	CSHL	ss3352061310	Nov 08, 2017 (151)
40	ILLUMINA	ss3627827741	Oct 12, 2018 (152)
41	ILLUMINA	ss3631459301	Oct 12, 2018 (152)
42	ILLUMINA	ss3642032911	Oct 12, 2018 (152)
43	URBANLAB	ss3650807522	Oct 12, 2018 (152)
44	EGCUT_WGS	ss3683505046	Jul 13, 2019 (153)
45	EVA_DECODE	ss3701820140	Jul 13, 2019 (153)
46	ACPOP	ss3742614549	Jul 13, 2019 (153)
47	EVA	ss3755491782	Jul 13, 2019 (153)
48	KHV_HUMAN_GENOMES	ss3820746808	Jul 13, 2019 (153)
49	EVA	ss3835210882	Apr 27, 2020 (154)
50	SGDP_PRJ	ss3887185130	Apr 27, 2020 (154)
51	KRGDB	ss3937076703	Apr 27, 2020 (154)
52	TOPMED	ss5059563517	Apr 27, 2021 (155)
53	TOMMO_GENOMICS	ss5225535007	Apr 27, 2021 (155)
54	1000G_HIGH_COVERAGE	ss5305573241	Oct 16, 2022 (156)
55	EVA	ss5315939409	Oct 16, 2022 (156)
56	EVA	ss5431940462	Oct 16, 2022 (156)
57	HUGCELL_USP	ss5498314100	Oct 16, 2022 (156)
58	EVA	ss5511969355	Oct 16, 2022 (156)
59	1000G_HIGH_COVERAGE	ss5610559726	Oct 16, 2022 (156)
60	SANFORD_IMAGENETICS	ss5661453776	Oct 16, 2022 (156)
61	TOMMO_GENOMICS	ss5783431849	Oct 16, 2022 (156)
62	YY_MCH	ss5817168852	Oct 16, 2022 (156)
63	EVA	ss5827656789	Oct 16, 2022 (156)
64	EVA	ss5874411110	Oct 16, 2022 (156)
65	EVA	ss5952879896	Oct 16, 2022 (156)
66	1000Genomes	NC_000018.9 - 56696888	Oct 12, 2018 (152)
67	1000Genomes_30x	NC_000018.10 - 59029656	Oct 16, 2022 (156)
68	The Avon Longitudinal Study of Parents and Children	NC_000018.9 - 56696888	Oct 12, 2018 (152)
69	Genetic variation in the Estonian population	NC_000018.9 - 56696888	Oct 12, 2018 (152)
70	The Danish reference pan genome	NC_000018.9 - 56696888	Apr 27, 2020 (154)
71	gnomAD - Genomes	NC_000018.10 - 59029656	Apr 27, 2021 (155)
72	Genome of the Netherlands Release 5	NC_000018.9 - 56696888	Apr 27, 2020 (154)
73	HapMap	NC_000018.10 - 59029656	Apr 27, 2020 (154)
74	KOREAN population from KRGDB	NC_000018.9 - 56696888	Apr 27, 2020 (154)
75	Northern Sweden	NC_000018.9 - 56696888	Jul 13, 2019 (153)
76	Qatari	NC_000018.9 - 56696888	Apr 27, 2020 (154)
77	SGDP_PRJ	NC_000018.9 - 56696888	Apr 27, 2020 (154)
78	Siberian	NC_000018.9 - 56696888	Apr 27, 2020 (154)
79	8.3KJPN	NC_000018.9 - 56696888	Apr 27, 2021 (155)
80	14KJPN	NC_000018.10 - 59029656	Oct 16, 2022 (156)
81	TopMed	NC_000018.10 - 59029656	Apr 27, 2021 (155)
82	UK 10K study - Twins	NC_000018.9 - 56696888	Oct 12, 2018 (152)
83	A Vietnamese Genetic Variation Database	NC_000018.9 - 56696888	Jul 13, 2019 (153)
84	ALFA	NC_000018.10 - 59029656	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)
rs60639891	May 26, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss78464694, ss84075136, ss90812050, ss117898314, ss168334504, ss255709603, ss292084082, ss483749491, ss1697875138	NC_000018.8:54847867:A:G	NC_000018.10:59029655:A:G	(self)
74688595, 41393324, 29243294, 4629198, 18439220, 44254097, 15899414, 19322625, 39202110, 10434672, 83504314, 41393324, 9144905, ss227902941, ss237498538, ss484305830, ss536489844, ss565691494, ss661527130, ss780604068, ss782599110, ss836097264, ss993813285, ss1081562773, ss1361347974, ss1428243990, ss1578438599, ss1637052418, ss1680046451, ss1809086348, ss1937280703, ss1968543332, ss2029410959, ss2157918318, ss2633483159, ss2702509826, ss2957598952, ss3016658026, ss3352061310, ss3627827741, ss3631459301, ss3642032911, ss3683505046, ss3742614549, ss3755491782, ss3835210882, ss3887185130, ss3937076703, ss5225535007, ss5315939409, ss5431940462, ss5511969355, ss5661453776, ss5827656789, ss5952879896	NC_000018.9:56696887:A:G	NC_000018.10:59029655:A:G	(self)
98085661, 526876187, 1618816, 117268953, 275109180, 9665542585, ss2222245260, ss3650807522, ss3701820140, ss3820746808, ss5059563517, ss5305573241, ss5498314100, ss5610559726, ss5783431849, ss5817168852, ss5874411110	NC_000018.10:59029655:A:G	NC_000018.10:59029655:A:G	(self)
ss21441772	NT_025028.13:4487733:A:G	NC_000018.10:59029655:A:G	(self)
ss44131143, ss132696674	NT_025028.14:4487751:A:G	NC_000018.10:59029655:A: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 rs12954864

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

rs12954864