Name: rs1952142
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.

rs1952142

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:69483171 (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>G
Variation Type: SNV Single Nucleotide Variation
Frequency: C=0.259598 (68713/264690, TOPMED)
C=0.265861 (37195/139904, GnomAD)
C=0.19853 (5610/28258, 14KJPN) (+ 15 more)
C=0.26173 (4944/18890, ALFA)
C=0.19934 (3341/16760, 8.3KJPN)
C=0.2745 (1758/6404, 1000G_30x)
C=0.2688 (1346/5008, 1000G)
C=0.2723 (1220/4480, Estonian)
C=0.1795 (526/2930, KOREAN)
C=0.2495 (472/1892, HapMap)
C=0.1790 (328/1832, Korea1K)
C=0.267 (266/998, GoNL)
C=0.288 (173/600, NorthernSweden)
C=0.211 (105/498, SGDP_PRJ)
C=0.236 (51/216, Qatari)
C=0.085 (18/212, Vietnamese)
C=0.20 (10/50, Siberian)
C=0.30 (12/40, GENOME_DK)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: LOC105378789 : 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	18890	C=0.26173	G=0.73827
European	Sub	14286	C=0.25899	G=0.74101
African	Sub	2946	C=0.2845	G=0.7155
African Others	Sub	114	C=0.307	G=0.693
African American	Sub	2832	C=0.2835	G=0.7165
Asian	Sub	112	C=0.179	G=0.821
East Asian	Sub	86	C=0.20	G=0.80
Other Asian	Sub	26	C=0.12	G=0.88
Latin American 1	Sub	146	C=0.178	G=0.822
Latin American 2	Sub	610	C=0.238	G=0.762
South Asian	Sub	98	C=0.36	G=0.64
Other	Sub	692	C=0.260	G=0.740

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=0.259598	G=0.740402
gnomAD - Genomes	Global	Study-wide	139904	C=0.265861	G=0.734139
gnomAD - Genomes	European	Sub	75804	C=0.26276	G=0.73724
gnomAD - Genomes	African	Sub	41926	C=0.28073	G=0.71927
gnomAD - Genomes	American	Sub	13588	C=0.25405	G=0.74595
gnomAD - Genomes	Ashkenazi Jewish	Sub	3320	C=0.2991	G=0.7009
gnomAD - Genomes	East Asian	Sub	3118	C=0.1616	G=0.8384
gnomAD - Genomes	Other	Sub	2148	C=0.2598	G=0.7402
14KJPN	JAPANESE	Study-wide	28258	C=0.19853	G=0.80147
Allele Frequency Aggregator	Total	Global	18890	C=0.26173	G=0.73827
Allele Frequency Aggregator	European	Sub	14286	C=0.25899	G=0.74101
Allele Frequency Aggregator	African	Sub	2946	C=0.2845	G=0.7155
Allele Frequency Aggregator	Other	Sub	692	C=0.260	G=0.740
Allele Frequency Aggregator	Latin American 2	Sub	610	C=0.238	G=0.762
Allele Frequency Aggregator	Latin American 1	Sub	146	C=0.178	G=0.822
Allele Frequency Aggregator	Asian	Sub	112	C=0.179	G=0.821
Allele Frequency Aggregator	South Asian	Sub	98	C=0.36	G=0.64
8.3KJPN	JAPANESE	Study-wide	16760	C=0.19934	G=0.80066
1000Genomes_30x	Global	Study-wide	6404	C=0.2745	G=0.7255
1000Genomes_30x	African	Sub	1786	C=0.2984	G=0.7016
1000Genomes_30x	Europe	Sub	1266	C=0.2543	G=0.7457
1000Genomes_30x	South Asian	Sub	1202	C=0.3719	G=0.6281
1000Genomes_30x	East Asian	Sub	1170	C=0.1615	G=0.8385
1000Genomes_30x	American	Sub	980	C=0.272	G=0.728
1000Genomes	Global	Study-wide	5008	C=0.2688	G=0.7312
1000Genomes	African	Sub	1322	C=0.2859	G=0.7141
1000Genomes	East Asian	Sub	1008	C=0.1647	G=0.8353
1000Genomes	Europe	Sub	1006	C=0.2575	G=0.7425
1000Genomes	South Asian	Sub	978	C=0.370	G=0.630
1000Genomes	American	Sub	694	C=0.261	G=0.739
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.2723	G=0.7277
KOREAN population from KRGDB	KOREAN	Study-wide	2930	C=0.1795	G=0.8205
HapMap	Global	Study-wide	1892	C=0.2495	G=0.7505
HapMap	American	Sub	770	C=0.251	G=0.749
HapMap	African	Sub	692	C=0.264	G=0.736
HapMap	Asian	Sub	254	C=0.228	G=0.772
HapMap	Europe	Sub	176	C=0.216	G=0.784
Korean Genome Project	KOREAN	Study-wide	1832	C=0.1790	G=0.8210
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.267	G=0.733
Northern Sweden	ACPOP	Study-wide	600	C=0.288	G=0.712
SGDP_PRJ	Global	Study-wide	498	C=0.211	G=0.789
Qatari	Global	Study-wide	216	C=0.236	G=0.764
A Vietnamese Genetic Variation Database	Global	Study-wide	212	C=0.085	G=0.915
Siberian	Global	Study-wide	50	C=0.20	G=0.80
The Danish reference pan genome	Danish	Study-wide	40	C=0.30	G=0.70

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.69483171C>A
GRCh38.p14 chr 1	NC_000001.11:g.69483171C>G
GRCh37.p13 chr 1	NC_000001.10:g.69948854C>A
GRCh37.p13 chr 1	NC_000001.10:g.69948854C>G

Gene: LOC105378789, uncharacterized LOC105378789 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC105378789 transcript variant X1	XR_001738106.2:n.	N/A	Intron Variant
LOC105378789 transcript variant X3	XR_007066165.1:n.	N/A	Intron Variant
LOC105378789 transcript variant X4	XR_007066166.1:n.	N/A	Intron Variant
LOC105378789 transcript variant X2	XR_947488.3: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	C=	A	G
GRCh38.p14 chr 1	NC_000001.11:g.69483171=	NC_000001.11:g.69483171C>A	NC_000001.11:g.69483171C>G
GRCh37.p13 chr 1	NC_000001.10:g.69948854=	NC_000001.10:g.69948854C>A	NC_000001.10:g.69948854C>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#.

83 SubSNP, 22 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	TSC-CSHL	ss2846456	Jan 12, 2001 (92)
2	WI_SSAHASNP	ss6399830	Feb 20, 2003 (111)
3	SC_SNP	ss13405668	Dec 05, 2003 (119)
4	CSHL-HAPMAP	ss16429447	Feb 27, 2004 (120)
5	SSAHASNP	ss20484719	Apr 05, 2004 (121)
6	PERLEGEN	ss23695214	Sep 20, 2004 (123)
7	AFFY	ss66146290	Dec 01, 2006 (127)
8	AFFY	ss76169679	Dec 07, 2007 (129)
9	HGSV	ss78522937	Dec 07, 2007 (129)
10	HGSV	ss80758096	Dec 15, 2007 (130)
11	KRIBB_YJKIM	ss81638532	Dec 15, 2007 (130)
12	HUMANGENOME_JCVI	ss97945403	Feb 06, 2009 (130)
13	BGI	ss102750562	Dec 01, 2009 (131)
14	1000GENOMES	ss108290034	Jan 23, 2009 (130)
15	1000GENOMES	ss110604108	Jan 25, 2009 (130)
16	ILLUMINA-UK	ss118783253	Feb 14, 2009 (130)
17	ENSEMBL	ss138909128	Dec 01, 2009 (131)
18	GMI	ss155144403	Dec 01, 2009 (131)
19	COMPLETE_GENOMICS	ss163490196	Jul 04, 2010 (132)
20	COMPLETE_GENOMICS	ss164502460	Jul 04, 2010 (132)
21	AFFY	ss172699434	Jul 04, 2010 (132)
22	BUSHMAN	ss198589024	Jul 04, 2010 (132)
23	BCM-HGSC-SUB	ss205070869	Jul 04, 2010 (132)
24	1000GENOMES	ss218440754	Jul 14, 2010 (132)
25	1000GENOMES	ss230575377	Jul 14, 2010 (132)
26	1000GENOMES	ss238261699	Jul 15, 2010 (132)
27	GMI	ss275866493	May 04, 2012 (137)
28	GMI	ss284068046	Apr 25, 2013 (138)
29	PJP	ss290532253	May 09, 2011 (134)
30	TISHKOFF	ss554223929	Apr 25, 2013 (138)
31	SSMP	ss648105008	Apr 25, 2013 (138)
32	EVA-GONL	ss975265220	Aug 21, 2014 (142)
33	JMKIDD_LAB	ss1067968152	Aug 21, 2014 (142)
34	1000GENOMES	ss1291293626	Aug 21, 2014 (142)
35	DDI	ss1425843468	Apr 01, 2015 (144)
36	EVA_GENOME_DK	ss1574131531	Apr 01, 2015 (144)
37	EVA_DECODE	ss1584635703	Apr 01, 2015 (144)
38	EVA_UK10K_ALSPAC	ss1600387590	Apr 01, 2015 (144)
39	EVA_UK10K_ALSPAC	ss1600387591	Apr 01, 2015 (144)
40	EVA_UK10K_TWINSUK	ss1643381623	Apr 01, 2015 (144)
41	EVA_UK10K_TWINSUK	ss1643381624	Apr 01, 2015 (144)
42	EVA_SVP	ss1712341589	Apr 01, 2015 (144)
43	HAMMER_LAB	ss1794518979	Sep 08, 2015 (146)
44	WEILL_CORNELL_DGM	ss1918472776	Feb 12, 2016 (147)
45	GENOMED	ss1966770921	Jul 19, 2016 (147)
46	JJLAB	ss2019753805	Sep 14, 2016 (149)
47	USC_VALOUEV	ss2147770153	Dec 20, 2016 (150)
48	HUMAN_LONGEVITY	ss2163340711	Dec 20, 2016 (150)
49	SYSTEMSBIOZJU	ss2624390290	Nov 08, 2017 (151)
50	GRF	ss2697688789	Nov 08, 2017 (151)
51	GNOMAD	ss2756281323	Nov 08, 2017 (151)
52	SWEGEN	ss2986976393	Nov 08, 2017 (151)
53	BIOINF_KMB_FNS_UNIBA	ss3023638924	Nov 08, 2017 (151)
54	CSHL	ss3343500947	Nov 08, 2017 (151)
55	URBANLAB	ss3646685109	Oct 11, 2018 (152)
56	EGCUT_WGS	ss3655048418	Jul 12, 2019 (153)
57	EVA_DECODE	ss3686968645	Jul 12, 2019 (153)
58	ACPOP	ss3727134936	Jul 12, 2019 (153)
59	EVA	ss3746327779	Jul 12, 2019 (153)
60	PACBIO	ss3783438134	Jul 12, 2019 (153)
61	PACBIO	ss3789092037	Jul 12, 2019 (153)
62	PACBIO	ss3793964781	Jul 12, 2019 (153)
63	KHV_HUMAN_GENOMES	ss3799334097	Jul 12, 2019 (153)
64	EVA	ss3826223694	Apr 25, 2020 (154)
65	EVA	ss3836499321	Apr 25, 2020 (154)
66	EVA	ss3841905982	Apr 25, 2020 (154)
67	SGDP_PRJ	ss3849056593	Apr 25, 2020 (154)
68	KRGDB	ss3894087782	Apr 25, 2020 (154)
69	KOGIC	ss3944707639	Apr 25, 2020 (154)
70	TOPMED	ss4453288906	Apr 25, 2021 (155)
71	TOMMO_GENOMICS	ss5144397532	Apr 25, 2021 (155)
72	1000G_HIGH_COVERAGE	ss5242616809	Oct 12, 2022 (156)
73	EVA	ss5319369630	Oct 12, 2022 (156)
74	HUGCELL_USP	ss5443645639	Oct 12, 2022 (156)
75	EVA	ss5505886180	Oct 12, 2022 (156)
76	1000G_HIGH_COVERAGE	ss5515070921	Oct 12, 2022 (156)
77	SANFORD_IMAGENETICS	ss5625728638	Oct 12, 2022 (156)
78	TOMMO_GENOMICS	ss5669297802	Oct 12, 2022 (156)
79	YY_MCH	ss5800683233	Oct 12, 2022 (156)
80	EVA	ss5832094757	Oct 12, 2022 (156)
81	EVA	ss5848949004	Oct 12, 2022 (156)
82	EVA	ss5908662588	Oct 12, 2022 (156)
83	EVA	ss5937568506	Oct 12, 2022 (156)
84	1000Genomes	NC_000001.10 - 69948854	Oct 11, 2018 (152)
85	1000Genomes_30x	NC_000001.11 - 69483171	Oct 12, 2022 (156)
86	The Avon Longitudinal Study of Parents and Children Submission ignored due to conflicting rows: Row 1111239 (NC_000001.10:69948853:C:C 1025/3854, NC_000001.10:69948853:C:G 2829/3854) Row 1111240 (NC_000001.10:69948853:C:C 3854/3854, NC_000001.10:69948853:C:A 0/3854)	-	Oct 11, 2018 (152)
87	The Avon Longitudinal Study of Parents and Children Submission ignored due to conflicting rows: Row 1111239 (NC_000001.10:69948853:C:C 1025/3854, NC_000001.10:69948853:C:G 2829/3854) Row 1111240 (NC_000001.10:69948853:C:C 3854/3854, NC_000001.10:69948853:C:A 0/3854)	-	Oct 11, 2018 (152)
88	Genetic variation in the Estonian population	NC_000001.10 - 69948854	Oct 11, 2018 (152)
89	The Danish reference pan genome	NC_000001.10 - 69948854	Apr 25, 2020 (154)
90	gnomAD - Genomes	NC_000001.11 - 69483171	Apr 25, 2021 (155)
91	Genome of the Netherlands Release 5	NC_000001.10 - 69948854	Apr 25, 2020 (154)
92	HapMap	NC_000001.11 - 69483171	Apr 25, 2020 (154)
93	KOREAN population from KRGDB	NC_000001.10 - 69948854	Apr 25, 2020 (154)
94	Korean Genome Project	NC_000001.11 - 69483171	Apr 25, 2020 (154)
95	Northern Sweden	NC_000001.10 - 69948854	Jul 12, 2019 (153)
96	Qatari	NC_000001.10 - 69948854	Apr 25, 2020 (154)
97	SGDP_PRJ	NC_000001.10 - 69948854	Apr 25, 2020 (154)
98	Siberian	NC_000001.10 - 69948854	Apr 25, 2020 (154)
99	8.3KJPN	NC_000001.10 - 69948854	Apr 25, 2021 (155)
100	14KJPN	NC_000001.11 - 69483171	Oct 12, 2022 (156)
101	TopMed	NC_000001.11 - 69483171	Apr 25, 2021 (155)
102	UK 10K study - Twins Submission ignored due to conflicting rows: Row 1111239 (NC_000001.10:69948853:C:C 941/3708, NC_000001.10:69948853:C:G 2767/3708) Row 1111240 (NC_000001.10:69948853:C:C 3707/3708, NC_000001.10:69948853:C:A 1/3708)	-	Oct 11, 2018 (152)
103	UK 10K study - Twins Submission ignored due to conflicting rows: Row 1111239 (NC_000001.10:69948853:C:C 941/3708, NC_000001.10:69948853:C:G 2767/3708) Row 1111240 (NC_000001.10:69948853:C:C 3707/3708, NC_000001.10:69948853:C:A 1/3708)	-	Oct 11, 2018 (152)
104	A Vietnamese Genetic Variation Database	NC_000001.10 - 69948854	Jul 12, 2019 (153)
105	ALFA	NC_000001.11 - 69483171	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)
rs60284823	May 25, 2008 (130)
rs60976895	Feb 27, 2009 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss1600387591, ss1643381624	NC_000001.10:69948853:C:A	NC_000001.11:69483170:C:A	(self)
ss78522937, ss80758096	NC_000001.8:69660874:C:G	NC_000001.11:69483170:C:G	(self)
ss66146290, ss76169679, ss108290034, ss110604108, ss118783253, ss163490196, ss164502460, ss172699434, ss198589024, ss205070869, ss275866493, ss284068046, ss290532253, ss1584635703, ss1712341589	NC_000001.9:69721441:C:G	NC_000001.11:69483170:C:G	(self)
2026370, 786666, 1543573, 474342, 1265176, 419801, 514706, 1073573, 286507, 2366839, 232913, ss218440754, ss230575377, ss238261699, ss554223929, ss648105008, ss975265220, ss1067968152, ss1291293626, ss1425843468, ss1574131531, ss1600387590, ss1643381623, ss1794518979, ss1918472776, ss1966770921, ss2019753805, ss2147770153, ss2624390290, ss2697688789, ss2756281323, ss2986976393, ss3343500947, ss3655048418, ss3727134936, ss3746327779, ss3783438134, ss3789092037, ss3793964781, ss3826223694, ss3836499321, ss3849056593, ss3894087782, ss5144397532, ss5319369630, ss5505886180, ss5625728638, ss5832094757, ss5937568506	NC_000001.10:69948853:C:G	NC_000001.11:69483170:C:G	(self)
2596856, 14292093, 91636, 1085640, 3134906, 16895241, 7863680405, ss2163340711, ss3023638924, ss3646685109, ss3686968645, ss3799334097, ss3841905982, ss3944707639, ss4453288906, ss5242616809, ss5443645639, ss5515070921, ss5669297802, ss5800683233, ss5848949004, ss5908662588	NC_000001.11:69483170:C:G	NC_000001.11:69483170:C:G	(self)
ss13405668	NT_004464.15:394144:C:G	NC_000001.11:69483170:C:G	(self)
ss16429447, ss20484719	NT_032977.6:31511922:C:G	NC_000001.11:69483170:C:G	(self)
ss2846456, ss6399830, ss23695214, ss81638532, ss97945403, ss102750562, ss138909128, ss155144403	NT_032977.9:39920771:C:G	NC_000001.11:69483170:C: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 rs1952142

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.

Choose placement

dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs1952142