Name: rs1048488
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.

rs1048488

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:825532 (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: C=0.285320 (39938/139976, GnomAD)
C=0.16254 (4593/28258, 14KJPN)
C=0.16193 (2714/16760, 8.3KJPN) (+ 14 more)
C=0.3024 (2702/8936, ALFA)
C=0.2764 (1770/6404, 1000G_30x)
C=0.2660 (1332/5008, 1000G)
C=0.1518 (585/3854, ALSPAC)
C=0.1578 (585/3708, TWINSUK)
C=0.1631 (478/2930, KOREAN)
C=0.3043 (574/1886, HapMap)
C=0.1643 (301/1832, Korea1K)
C=0.173 (173/998, GoNL)
C=0.148 (89/600, NorthernSweden)
C=0.166 (88/530, SGDP_PRJ)
C=0.241 (52/216, Qatari)
C=0.085 (18/212, Vietnamese)
C=0.05 (2/40, GENOME_DK)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: None
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	8936	C=0.3024	A=0.0000, T=0.6976
European	Sub	7030	C=0.2215	A=0.0000, T=0.7785
African	Sub	1238	C=0.7649	A=0.0000, T=0.2351
African Others	Sub	62	C=0.85	A=0.00, T=0.15
African American	Sub	1176	C=0.7602	A=0.0000, T=0.2398
Asian	Sub	14	C=0.21	A=0.00, T=0.79
East Asian	Sub	12	C=0.25	A=0.00, T=0.75
Other Asian	Sub	2	C=0.0	A=0.0, T=1.0
Latin American 1	Sub	36	C=0.64	A=0.00, T=0.36
Latin American 2	Sub	90	C=0.44	A=0.00, T=0.56
South Asian	Sub	2	C=1.0	A=0.0, T=0.0
Other	Sub	526	C=0.247	A=0.000, T=0.753

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
gnomAD - Genomes	Global	Study-wide	139976	C=0.285320	T=0.714680
gnomAD - Genomes	European	Sub	75820	C=0.17998	T=0.82002
gnomAD - Genomes	African	Sub	41914	C=0.52169	T=0.47831
gnomAD - Genomes	American	Sub	13642	C=0.20943	T=0.79057
gnomAD - Genomes	Ashkenazi Jewish	Sub	3318	C=0.2158	T=0.7842
gnomAD - Genomes	East Asian	Sub	3130	C=0.1026	T=0.8974
gnomAD - Genomes	Other	Sub	2152	C=0.2472	T=0.7528
14KJPN	JAPANESE	Study-wide	28258	C=0.16254	T=0.83746
8.3KJPN	JAPANESE	Study-wide	16760	C=0.16193	T=0.83807
Allele Frequency Aggregator	Total	Global	8936	C=0.3024	A=0.0000, T=0.6976
Allele Frequency Aggregator	European	Sub	7030	C=0.2215	A=0.0000, T=0.7785
Allele Frequency Aggregator	African	Sub	1238	C=0.7649	A=0.0000, T=0.2351
Allele Frequency Aggregator	Other	Sub	526	C=0.247	A=0.000, T=0.753
Allele Frequency Aggregator	Latin American 2	Sub	90	C=0.44	A=0.00, T=0.56
Allele Frequency Aggregator	Latin American 1	Sub	36	C=0.64	A=0.00, T=0.36
Allele Frequency Aggregator	Asian	Sub	14	C=0.21	A=0.00, T=0.79
Allele Frequency Aggregator	South Asian	Sub	2	C=1.0	A=0.0, T=0.0
1000Genomes_30x	Global	Study-wide	6404	C=0.2764	T=0.7236
1000Genomes_30x	African	Sub	1786	C=0.5605	T=0.4395
1000Genomes_30x	Europe	Sub	1266	C=0.1580	T=0.8420
1000Genomes_30x	South Asian	Sub	1202	C=0.1980	T=0.8020
1000Genomes_30x	East Asian	Sub	1170	C=0.1171	T=0.8829
1000Genomes_30x	American	Sub	980	C=0.198	T=0.802
1000Genomes	Global	Study-wide	5008	C=0.2660	T=0.7340
1000Genomes	African	Sub	1322	C=0.5552	T=0.4448
1000Genomes	East Asian	Sub	1008	C=0.1161	T=0.8839
1000Genomes	Europe	Sub	1006	C=0.1600	T=0.8400
1000Genomes	South Asian	Sub	978	C=0.189	T=0.811
1000Genomes	American	Sub	694	C=0.195	T=0.805
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.1518	T=0.8482
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.1578	T=0.8422
KOREAN population from KRGDB	KOREAN	Study-wide	2930	C=0.1631	T=0.8369
HapMap	Global	Study-wide	1886	C=0.3043	T=0.6957
HapMap	American	Sub	764	C=0.205	T=0.795
HapMap	African	Sub	692	C=0.523	T=0.477
HapMap	Asian	Sub	254	C=0.118	T=0.882
HapMap	Europe	Sub	176	C=0.142	T=0.858
Korean Genome Project	KOREAN	Study-wide	1832	C=0.1643	T=0.8357
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.173	T=0.827
Northern Sweden	ACPOP	Study-wide	600	C=0.148	T=0.852
SGDP_PRJ	Global	Study-wide	530	C=0.166	T=0.834
Qatari	Global	Study-wide	216	C=0.241	T=0.759
A Vietnamese Genetic Variation Database	Global	Study-wide	212	C=0.085	T=0.915
The Danish reference pan genome	Danish	Study-wide	40	C=0.05	T=0.95

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.825532C>A
GRCh38.p14 chr 1	NC_000001.11:g.825532C>T
GRCh37.p13 chr 1	NC_000001.10:g.760912C>A
GRCh37.p13 chr 1	NC_000001.10:g.760912C>T

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 1	NC_000001.11:g.825532=	NC_000001.11:g.825532C>A	NC_000001.11:g.825532C>T
GRCh37.p13 chr 1	NC_000001.10:g.760912=	NC_000001.10:g.760912C>A	NC_000001.10:g.760912C>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#.

78 SubSNP, 17 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_JCM	ss4358500	Mar 26, 2002 (103)
2	SC_JCM	ss6040318	Feb 20, 2003 (111)
3	WI_SSAHASNP	ss11348776	Jul 11, 2003 (117)
4	ILLUMINA	ss75004583	Dec 07, 2007 (129)
5	HGSV	ss78852399	Dec 07, 2007 (129)
6	BCMHGSC_JDW	ss87155773	Mar 23, 2008 (129)
7	HUMANGENOME_JCVI	ss97913205	Feb 04, 2009 (130)
8	BGI	ss105111678	Dec 01, 2009 (131)
9	1000GENOMES	ss107938275	Jan 22, 2009 (130)
10	1000GENOMES	ss109937276	Jan 24, 2009 (130)
11	ILLUMINA-UK	ss118438281	Feb 14, 2009 (130)
12	KRIBB_YJKIM	ss119380166	Dec 01, 2009 (131)
13	ENSEMBL	ss137752234	Dec 01, 2009 (131)
14	ENSEMBL	ss138897564	Dec 01, 2009 (131)
15	GMI	ss154522359	Dec 01, 2009 (131)
16	ILLUMINA	ss170151194	Jul 04, 2010 (132)
17	BUSHMAN	ss197885432	Jul 04, 2010 (132)
18	BCM-HGSC-SUB	ss205161238	Jul 04, 2010 (132)
19	1000GENOMES	ss218190389	Jul 14, 2010 (132)
20	1000GENOMES	ss230395469	Jul 14, 2010 (132)
21	1000GENOMES	ss238114976	Jul 15, 2010 (132)
22	BL	ss252864114	May 09, 2011 (134)
23	GMI	ss275680797	May 04, 2012 (137)
24	GMI	ss283987383	Apr 25, 2013 (138)
25	PJP	ss290493782	May 09, 2011 (134)
26	ILLUMINA	ss536609952	Sep 08, 2015 (146)
27	TISHKOFF	ss553710388	Apr 25, 2013 (138)
28	SSMP	ss647516153	Apr 25, 2013 (138)
29	EVA-GONL	ss974769293	Aug 21, 2014 (142)
30	JMKIDD_LAB	ss1067612337	Aug 21, 2014 (142)
31	1000GENOMES	ss1289339032	Aug 21, 2014 (142)
32	DDI	ss1425684826	Apr 01, 2015 (144)
33	EVA_GENOME_DK	ss1573851142	Apr 01, 2015 (144)
34	EVA_DECODE	ss1584129454	Apr 01, 2015 (144)
35	EVA_UK10K_ALSPAC	ss1599378343	Apr 01, 2015 (144)
36	EVA_UK10K_TWINSUK	ss1642372376	Apr 01, 2015 (144)
37	EVA_SVP	ss1712305458	Apr 01, 2015 (144)
38	HAMMER_LAB	ss1793705724	Sep 08, 2015 (146)
39	WEILL_CORNELL_DGM	ss1917960267	Feb 12, 2016 (147)
40	GENOMED	ss1966667322	Jul 19, 2016 (147)
41	JJLAB	ss2019498401	Sep 14, 2016 (149)
42	SYSTEMSBIOZJU	ss2624264760	Nov 08, 2017 (151)
43	GRF	ss2697374589	Nov 08, 2017 (151)
44	GNOMAD	ss2750637726	Nov 08, 2017 (151)
45	SWEGEN	ss2986148904	Nov 08, 2017 (151)
46	BIOINF_KMB_FNS_UNIBA	ss3023513710	Nov 08, 2017 (151)
47	CSHL	ss3343272530	Nov 08, 2017 (151)
48	ILLUMINA	ss3626006482	Oct 11, 2018 (152)
49	ILLUMINA	ss3637732360	Oct 11, 2018 (152)
50	ILLUMINA	ss3642746661	Oct 11, 2018 (152)
51	URBANLAB	ss3646581199	Oct 11, 2018 (152)
52	EVA_DECODE	ss3685992031	Jul 12, 2019 (153)
53	ACPOP	ss3726716325	Jul 12, 2019 (153)
54	EVA	ss3745720902	Jul 12, 2019 (153)
55	PACBIO	ss3783302121	Jul 12, 2019 (153)
56	PACBIO	ss3788979991	Jul 12, 2019 (153)
57	PACBIO	ss3793852527	Jul 12, 2019 (153)
58	KHV_HUMAN_GENOMES	ss3798743507	Jul 12, 2019 (153)
59	EVA	ss3825981445	Apr 25, 2020 (154)
60	EVA	ss3836378389	Apr 25, 2020 (154)
61	EVA	ss3841782390	Apr 25, 2020 (154)
62	SGDP_PRJ	ss3847995210	Apr 25, 2020 (154)
63	KRGDB	ss3892835577	Apr 25, 2020 (154)
64	KOGIC	ss3943629382	Apr 25, 2020 (154)
65	EVA	ss4016889035	Apr 25, 2021 (155)
66	TOMMO_GENOMICS	ss5142051703	Apr 25, 2021 (155)
67	1000G_HIGH_COVERAGE	ss5240863038	Oct 12, 2022 (156)
68	EVA	ss5316182875	Oct 12, 2022 (156)
69	HUGCELL_USP	ss5442112135	Oct 12, 2022 (156)
70	1000G_HIGH_COVERAGE	ss5512487570	Oct 12, 2022 (156)
71	SANFORD_IMAGENETICS	ss5624749023	Oct 12, 2022 (156)
72	TOMMO_GENOMICS	ss5666190908	Oct 12, 2022 (156)
73	YY_MCH	ss5800243639	Oct 12, 2022 (156)
74	EVA	ss5831418203	Oct 12, 2022 (156)
75	EVA	ss5848748861	Oct 12, 2022 (156)
76	EVA	ss5906704547	Oct 12, 2022 (156)
77	EVA	ss5936582490	Oct 12, 2022 (156)
78	EVA	ss5979259206	Oct 12, 2022 (156)
79	1000Genomes	NC_000001.10 - 760912	Oct 11, 2018 (152)
80	1000Genomes_30x	NC_000001.11 - 825532	Oct 12, 2022 (156)
81	The Avon Longitudinal Study of Parents and Children	NC_000001.10 - 760912	Oct 11, 2018 (152)
82	The Danish reference pan genome	NC_000001.10 - 760912	Apr 25, 2020 (154)
83	gnomAD - Genomes	NC_000001.11 - 825532	Apr 25, 2021 (155)
84	Genome of the Netherlands Release 5	NC_000001.10 - 760912	Apr 25, 2020 (154)
85	HapMap	NC_000001.11 - 825532	Apr 25, 2020 (154)
86	KOREAN population from KRGDB	NC_000001.10 - 760912	Apr 25, 2020 (154)
87	Korean Genome Project	NC_000001.11 - 825532	Apr 25, 2020 (154)
88	Northern Sweden	NC_000001.10 - 760912	Jul 12, 2019 (153)
89	Qatari	NC_000001.10 - 760912	Apr 25, 2020 (154)
90	SGDP_PRJ	NC_000001.10 - 760912	Apr 25, 2020 (154)
91	8.3KJPN	NC_000001.10 - 760912	Apr 25, 2021 (155)
92	14KJPN	NC_000001.11 - 825532	Oct 12, 2022 (156)
93	UK 10K study - Twins	NC_000001.10 - 760912	Oct 11, 2018 (152)
94	A Vietnamese Genetic Variation Database	NC_000001.10 - 760912	Jul 12, 2019 (153)
95	ALFA	NC_000001.11 - 825532	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)
rs3175776	Jul 03, 2002 (106)
rs4081590	Dec 16, 2002 (110)
rs7515682	Aug 27, 2003 (117)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
397932652	NC_000001.11:825531:C:A	NC_000001.11:825531:C:A	(self)
ss78852399	NC_000001.8:800774:C:T	NC_000001.11:825531:C:T	(self)
ss87155773, ss107938275, ss109937276, ss118438281, ss197885432, ss205161238, ss252864114, ss275680797, ss283987383, ss290493782, ss1584129454, ss1712305458, ss3642746661	NC_000001.9:750774:C:T	NC_000001.11:825531:C:T	(self)
3753, 239, 1358376, 365, 12971, 1190, 2197, 12190, 21010, 239, 48, ss218190389, ss230395469, ss238114976, ss536609952, ss553710388, ss647516153, ss974769293, ss1067612337, ss1289339032, ss1425684826, ss1573851142, ss1599378343, ss1642372376, ss1793705724, ss1917960267, ss1966667322, ss2019498401, ss2624264760, ss2697374589, ss2750637726, ss2986148904, ss3343272530, ss3626006482, ss3637732360, ss3726716325, ss3745720902, ss3783302121, ss3788979991, ss3793852527, ss3825981445, ss3836378389, ss3847995210, ss3892835577, ss4016889035, ss5142051703, ss5316182875, ss5624749023, ss5831418203, ss5936582490, ss5979259206	NC_000001.10:760911:C:T	NC_000001.11:825531:C:T	(self)
13505, 63120, 49, 7383, 28012, 397932652, ss3023513710, ss3646581199, ss3685992031, ss3798743507, ss3841782390, ss3943629382, ss5240863038, ss5442112135, ss5512487570, ss5666190908, ss5800243639, ss5848748861, ss5906704547	NC_000001.11:825531:C:T	NC_000001.11:825531:C:T	(self)
ss4358500, ss6040318, ss75004583, ss97913205, ss105111678, ss119380166, ss137752234, ss138897564, ss154522359, ss170151194	NT_004350.19:239543:C:T	NC_000001.11:825531:C:T	(self)
ss11348776	NT_034471.3:239543:C:T	NC_000001.11:825531: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 rs1048488

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

rs1048488