Name: rs12738089
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.

rs12738089

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:154631695 (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=0.218248 (57768/264690, TOPMED)
G=0.227502 (31858/140034, GnomAD)
G=0.13049 (3687/28256, 14KJPN) (+ 16 more)
G=0.22345 (4221/18890, ALFA)
G=0.13502 (2263/16760, 8.3KJPN)
G=0.2033 (1302/6404, 1000G_30x)
G=0.2027 (1015/5008, 1000G)
G=0.1902 (852/4480, Estonian)
G=0.2398 (924/3854, ALSPAC)
G=0.2325 (862/3708, TWINSUK)
G=0.1311 (383/2922, KOREAN)
G=0.1474 (270/1832, Korea1K)
G=0.237 (237/998, GoNL)
G=0.273 (164/600, NorthernSweden)
G=0.245 (53/216, Qatari)
G=0.067 (14/210, Vietnamese)
A=0.407 (83/204, SGDP_PRJ)
G=0.28 (11/40, GENOME_DK)
A=0.33 (10/30, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: LOC124904427 : Non Coding Transcript 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	A=0.77655	G=0.22345
European	Sub	14286	A=0.77124	G=0.22876
African	Sub	2946	A=0.7743	G=0.2257
African Others	Sub	114	A=0.772	G=0.228
African American	Sub	2832	A=0.7744	G=0.2256
Asian	Sub	112	A=0.848	G=0.152
East Asian	Sub	86	A=0.83	G=0.17
Other Asian	Sub	26	A=0.92	G=0.08
Latin American 1	Sub	146	A=0.808	G=0.192
Latin American 2	Sub	610	A=0.859	G=0.141
South Asian	Sub	98	A=0.85	G=0.15
Other	Sub	692	A=0.795	G=0.205

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=0.781752	G=0.218248
gnomAD - Genomes	Global	Study-wide	140034	A=0.772498	G=0.227502
gnomAD - Genomes	European	Sub	75850	A=0.75794	G=0.24206
gnomAD - Genomes	African	Sub	41956	A=0.78029	G=0.21971
gnomAD - Genomes	American	Sub	13626	A=0.80420	G=0.19580
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	A=0.7650	G=0.2350
gnomAD - Genomes	East Asian	Sub	3130	A=0.8936	G=0.1064
gnomAD - Genomes	Other	Sub	2148	A=0.7682	G=0.2318
14KJPN	JAPANESE	Study-wide	28256	A=0.86951	G=0.13049
Allele Frequency Aggregator	Total	Global	18890	A=0.77655	G=0.22345
Allele Frequency Aggregator	European	Sub	14286	A=0.77124	G=0.22876
Allele Frequency Aggregator	African	Sub	2946	A=0.7743	G=0.2257
Allele Frequency Aggregator	Other	Sub	692	A=0.795	G=0.205
Allele Frequency Aggregator	Latin American 2	Sub	610	A=0.859	G=0.141
Allele Frequency Aggregator	Latin American 1	Sub	146	A=0.808	G=0.192
Allele Frequency Aggregator	Asian	Sub	112	A=0.848	G=0.152
Allele Frequency Aggregator	South Asian	Sub	98	A=0.85	G=0.15
8.3KJPN	JAPANESE	Study-wide	16760	A=0.86498	G=0.13502
1000Genomes_30x	Global	Study-wide	6404	A=0.7967	G=0.2033
1000Genomes_30x	African	Sub	1786	A=0.7956	G=0.2044
1000Genomes_30x	Europe	Sub	1266	A=0.7306	G=0.2694
1000Genomes_30x	South Asian	Sub	1202	A=0.7970	G=0.2030
1000Genomes_30x	East Asian	Sub	1170	A=0.8675	G=0.1325
1000Genomes_30x	American	Sub	980	A=0.799	G=0.201
1000Genomes	Global	Study-wide	5008	A=0.7973	G=0.2027
1000Genomes	African	Sub	1322	A=0.7890	G=0.2110
1000Genomes	East Asian	Sub	1008	A=0.8671	G=0.1329
1000Genomes	Europe	Sub	1006	A=0.7316	G=0.2684
1000Genomes	South Asian	Sub	978	A=0.796	G=0.204
1000Genomes	American	Sub	694	A=0.810	G=0.190
Genetic variation in the Estonian population	Estonian	Study-wide	4480	A=0.8098	G=0.1902
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.7602	G=0.2398
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.7675	G=0.2325
KOREAN population from KRGDB	KOREAN	Study-wide	2922	A=0.8689	G=0.1311
Korean Genome Project	KOREAN	Study-wide	1832	A=0.8526	G=0.1474
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	A=0.763	G=0.237
Northern Sweden	ACPOP	Study-wide	600	A=0.727	G=0.273
Qatari	Global	Study-wide	216	A=0.755	G=0.245
A Vietnamese Genetic Variation Database	Global	Study-wide	210	A=0.933	G=0.067
SGDP_PRJ	Global	Study-wide	204	A=0.407	G=0.593
The Danish reference pan genome	Danish	Study-wide	40	A=0.72	G=0.28
Siberian	Global	Study-wide	30	A=0.33	G=0.67

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.154631695A>G
GRCh37.p13 chr 1	NC_000001.10:g.154604171A>G
ADAR RefSeqGene (LRG_1212)	NG_011844.2:g.4866T>C

Gene: LOC124904427, uncharacterized LOC124904427 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC124904427 transcript variant X1	XR_007066635.1:n.250A>G	N/A	Non Coding Transcript 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 1	NC_000001.11:g.154631695=	NC_000001.11:g.154631695A>G
GRCh37.p13 chr 1	NC_000001.10:g.154604171=	NC_000001.10:g.154604171A>G
ADAR RefSeqGene (LRG_1212)	NG_011844.2:g.4866=	NG_011844.2:g.4866T>C
LOC124904427 transcript variant X1	XR_007066635.1:n.250=	XR_007066635.1:n.250A>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#.

60 SubSNP, 19 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SSAHASNP	ss20503374	Apr 05, 2004 (121)
2	ABI	ss41194005	Mar 13, 2006 (126)
3	HUMANGENOME_JCVI	ss99251175	Feb 04, 2009 (130)
4	1000GENOMES	ss108599713	Jan 23, 2009 (130)
5	ILLUMINA-UK	ss119032505	Feb 15, 2009 (130)
6	ENSEMBL	ss139210543	Dec 01, 2009 (131)
7	GMI	ss155753257	Dec 01, 2009 (131)
8	COMPLETE_GENOMICS	ss167134245	Jul 04, 2010 (132)
9	1000GENOMES	ss218651440	Jul 14, 2010 (132)
10	1000GENOMES	ss230732075	Jul 14, 2010 (132)
11	1000GENOMES	ss238379962	Jul 15, 2010 (132)
12	BL	ss253509541	May 09, 2011 (134)
13	GMI	ss276051373	May 04, 2012 (137)
14	PJP	ss290637159	May 09, 2011 (134)
15	TISHKOFF	ss554694097	Apr 25, 2013 (138)
16	SSMP	ss648414218	Apr 25, 2013 (138)
17	EVA-GONL	ss975682892	Aug 21, 2014 (142)
18	JMKIDD_LAB	ss1068269877	Aug 21, 2014 (142)
19	1000GENOMES	ss1292926970	Aug 21, 2014 (142)
20	DDI	ss1425979084	Apr 01, 2015 (144)
21	EVA_GENOME_DK	ss1574392334	Apr 01, 2015 (144)
22	EVA_DECODE	ss1585064357	Apr 01, 2015 (144)
23	EVA_UK10K_ALSPAC	ss1601214769	Apr 01, 2015 (144)
24	EVA_UK10K_TWINSUK	ss1644208802	Apr 01, 2015 (144)
25	HAMMER_LAB	ss1795092480	Sep 08, 2015 (146)
26	WEILL_CORNELL_DGM	ss1918916810	Feb 12, 2016 (147)
27	JJLAB	ss2019973953	Sep 14, 2016 (149)
28	USC_VALOUEV	ss2147998480	Dec 20, 2016 (150)
29	HUMAN_LONGEVITY	ss2166544043	Dec 20, 2016 (150)
30	GRF	ss2697971395	Nov 08, 2017 (151)
31	GNOMAD	ss2761319874	Nov 08, 2017 (151)
32	SWEGEN	ss2987752663	Nov 08, 2017 (151)
33	BIOINF_KMB_FNS_UNIBA	ss3023744169	Nov 08, 2017 (151)
34	CSHL	ss3343710696	Nov 08, 2017 (151)
35	URBANLAB	ss3646791450	Oct 11, 2018 (152)
36	EGCUT_WGS	ss3655692893	Jul 12, 2019 (153)
37	EVA_DECODE	ss3687783080	Jul 12, 2019 (153)
38	ACPOP	ss3727486031	Jul 12, 2019 (153)
39	EVA	ss3746808529	Jul 12, 2019 (153)
40	KHV_HUMAN_GENOMES	ss3799810189	Jul 12, 2019 (153)
41	EVA	ss3826424342	Apr 25, 2020 (154)
42	EVA	ss3836606778	Apr 25, 2020 (154)
43	EVA	ss3842016004	Apr 25, 2020 (154)
44	SGDP_PRJ	ss3850007223	Apr 25, 2020 (154)
45	KRGDB	ss3895213790	Apr 25, 2020 (154)
46	KOGIC	ss3945652004	Apr 25, 2020 (154)
47	TOPMED	ss4468315041	Apr 25, 2021 (155)
48	TOMMO_GENOMICS	ss5146484819	Apr 25, 2021 (155)
49	1000G_HIGH_COVERAGE	ss5244294193	Oct 12, 2022 (156)
50	EVA	ss5322052046	Oct 12, 2022 (156)
51	HUGCELL_USP	ss5444887554	Oct 12, 2022 (156)
52	EVA	ss5506029351	Oct 12, 2022 (156)
53	1000G_HIGH_COVERAGE	ss5517622956	Oct 12, 2022 (156)
54	SANFORD_IMAGENETICS	ss5626592083	Oct 12, 2022 (156)
55	TOMMO_GENOMICS	ss5673680967	Oct 12, 2022 (156)
56	YY_MCH	ss5801260436	Oct 12, 2022 (156)
57	EVA	ss5832665994	Oct 12, 2022 (156)
58	EVA	ss5849109079	Oct 12, 2022 (156)
59	EVA	ss5910247171	Oct 12, 2022 (156)
60	EVA	ss5938385979	Oct 12, 2022 (156)
61	1000Genomes	NC_000001.10 - 154604171	Oct 11, 2018 (152)
62	1000Genomes_30x	NC_000001.11 - 154631695	Oct 12, 2022 (156)
63	The Avon Longitudinal Study of Parents and Children	NC_000001.10 - 154604171	Oct 11, 2018 (152)
64	Genetic variation in the Estonian population	NC_000001.10 - 154604171	Oct 11, 2018 (152)
65	The Danish reference pan genome	NC_000001.10 - 154604171	Apr 25, 2020 (154)
66	gnomAD - Genomes	NC_000001.11 - 154631695	Apr 25, 2021 (155)
67	Genome of the Netherlands Release 5	NC_000001.10 - 154604171	Apr 25, 2020 (154)
68	KOREAN population from KRGDB	NC_000001.10 - 154604171	Apr 25, 2020 (154)
69	Korean Genome Project	NC_000001.11 - 154631695	Apr 25, 2020 (154)
70	Northern Sweden	NC_000001.10 - 154604171	Jul 12, 2019 (153)
71	Qatari	NC_000001.10 - 154604171	Apr 25, 2020 (154)
72	SGDP_PRJ	NC_000001.10 - 154604171	Apr 25, 2020 (154)
73	Siberian	NC_000001.10 - 154604171	Apr 25, 2020 (154)
74	8.3KJPN	NC_000001.10 - 154604171	Apr 25, 2021 (155)
75	14KJPN	NC_000001.11 - 154631695	Oct 12, 2022 (156)
76	TopMed	NC_000001.11 - 154631695	Apr 25, 2021 (155)
77	UK 10K study - Twins	NC_000001.10 - 154604171	Oct 11, 2018 (152)
78	A Vietnamese Genetic Variation Database	NC_000001.10 - 154604171	Jul 12, 2019 (153)
79	ALFA	NC_000001.11 - 154631695	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).

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss108599713, ss119032505, ss167134245, ss253509541, ss276051373, ss290637159, ss1585064357	NC_000001.9:152870794:A:G	NC_000001.11:154631694:A:G	(self)
3719100, 2022108, 1431141, 1708789, 878527, 2391184, 770896, 958740, 2024203, 514834, 4454126, 2022108, 434568, ss218651440, ss230732075, ss238379962, ss554694097, ss648414218, ss975682892, ss1068269877, ss1292926970, ss1425979084, ss1574392334, ss1601214769, ss1644208802, ss1795092480, ss1918916810, ss2019973953, ss2147998480, ss2697971395, ss2761319874, ss2987752663, ss3343710696, ss3655692893, ss3727486031, ss3746808529, ss3826424342, ss3836606778, ss3850007223, ss3895213790, ss5146484819, ss5322052046, ss5506029351, ss5626592083, ss5832665994, ss5938385979	NC_000001.10:154604170:A:G	NC_000001.11:154631694:A:G	(self)
5148891, 27061635, 2030005, 7518071, 31921376, 7967042071, ss2166544043, ss3023744169, ss3646791450, ss3687783080, ss3799810189, ss3842016004, ss3945652004, ss4468315041, ss5244294193, ss5444887554, ss5517622956, ss5673680967, ss5801260436, ss5849109079, ss5910247171	NC_000001.11:154631694:A:G	NC_000001.11:154631694:A:G	(self)
ss41194005, ss99251175, ss139210543, ss155753257	NT_004487.19:6092812:A:G	NC_000001.11:154631694:A:G	(self)
ss20503374	NT_079484.1:1054002:A:G	NC_000001.11:154631694: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 rs12738089

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

rs12738089