Name: rs1059774
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.

rs1059774

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr15:22825366 (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: G=0.358805 (94972/264690, TOPMED)
C=0.37097 (29187/78678, PAGE_STUDY)
C=0.46797 (13224/28258, 14KJPN) (+ 16 more)
C=0.46933 (7866/16760, 8.3KJPN)
G=0.23264 (3257/14000, ALFA)
G=0.4037 (2585/6404, 1000G_30x)
G=0.4101 (2054/5008, 1000G)
G=0.3371 (1510/4480, Estonian)
G=0.3949 (1522/3854, ALSPAC)
G=0.3959 (1468/3708, TWINSUK)
C=0.4628 (1356/2930, KOREAN)
G=0.3080 (494/1604, HapMap)
G=0.388 (387/998, GoNL)
G=0.413 (248/600, NorthernSweden)
C=0.253 (98/388, SGDP_PRJ)
G=0.398 (86/216, Qatari)
C=0.354 (75/212, Vietnamese)
G=0.42 (17/40, GENOME_DK)
C=0.28 (9/32, Siberian)

Clinical Significance: Reported in ClinVar
Gene : Consequence: NIPA1 : 3 Prime UTR 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	14000	C=0.76736	A=0.00000, G=0.23264
European	Sub	11090	C=0.72480	A=0.00000, G=0.27520
African	Sub	2282	C=0.9566	A=0.0000, G=0.0434
African Others	Sub	98	C=0.98	A=0.00, G=0.02
African American	Sub	2184	C=0.9556	A=0.0000, G=0.0444
Asian	Sub	26	C=0.96	A=0.00, G=0.04
East Asian	Sub	18	C=1.00	A=0.00, G=0.00
Other Asian	Sub	8	C=0.9	A=0.0, G=0.1
Latin American 1	Sub	46	C=1.00	A=0.00, G=0.00
Latin American 2	Sub	72	C=1.00	A=0.00, G=0.00
South Asian	Sub	34	C=0.91	A=0.00, G=0.09
Other	Sub	450	C=0.773	A=0.000, G=0.227

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=0.641195	G=0.358805
The PAGE Study	Global	Study-wide	78678	C=0.37097	G=0.62903
The PAGE Study	AfricanAmerican	Sub	32510	C=0.16032	G=0.83968
The PAGE Study	Mexican	Sub	10802	C=0.65219	G=0.34781
The PAGE Study	Asian	Sub	8312	C=0.5454	G=0.4546
The PAGE Study	PuertoRican	Sub	7918	C=0.4184	G=0.5816
The PAGE Study	NativeHawaiian	Sub	4530	C=0.5457	G=0.4543
The PAGE Study	Cuban	Sub	4230	C=0.3903	G=0.6097
The PAGE Study	Dominican	Sub	3828	C=0.3028	G=0.6972
The PAGE Study	CentralAmerican	Sub	2450	C=0.6171	G=0.3829
The PAGE Study	SouthAmerican	Sub	1982	C=0.6413	G=0.3587
The PAGE Study	NativeAmerican	Sub	1260	C=0.4444	G=0.5556
The PAGE Study	SouthAsian	Sub	856	C=0.536	G=0.464
14KJPN	JAPANESE	Study-wide	28258	C=0.46797	G=0.53203
8.3KJPN	JAPANESE	Study-wide	16760	C=0.46933	G=0.53067
Allele Frequency Aggregator	Total	Global	14000	C=0.76736	A=0.00000, G=0.23264
Allele Frequency Aggregator	European	Sub	11090	C=0.72480	A=0.00000, G=0.27520
Allele Frequency Aggregator	African	Sub	2282	C=0.9566	A=0.0000, G=0.0434
Allele Frequency Aggregator	Other	Sub	450	C=0.773	A=0.000, G=0.227
Allele Frequency Aggregator	Latin American 2	Sub	72	C=1.00	A=0.00, G=0.00
Allele Frequency Aggregator	Latin American 1	Sub	46	C=1.00	A=0.00, G=0.00
Allele Frequency Aggregator	South Asian	Sub	34	C=0.91	A=0.00, G=0.09
Allele Frequency Aggregator	Asian	Sub	26	C=0.96	A=0.00, G=0.04
1000Genomes_30x	Global	Study-wide	6404	C=0.5963	G=0.4037
1000Genomes_30x	African	Sub	1786	C=0.8970	G=0.1030
1000Genomes_30x	Europe	Sub	1266	C=0.6240	G=0.3760
1000Genomes_30x	South Asian	Sub	1202	C=0.4700	G=0.5300
1000Genomes_30x	East Asian	Sub	1170	C=0.4051	G=0.5949
1000Genomes_30x	American	Sub	980	C=0.396	G=0.604
1000Genomes	Global	Study-wide	5008	C=0.5899	G=0.4101
1000Genomes	African	Sub	1322	C=0.8911	G=0.1089
1000Genomes	East Asian	Sub	1008	C=0.4107	G=0.5893
1000Genomes	Europe	Sub	1006	C=0.6312	G=0.3688
1000Genomes	South Asian	Sub	978	C=0.463	G=0.537
1000Genomes	American	Sub	694	C=0.395	G=0.605
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.6629	G=0.3371
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.6051	G=0.3949
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.6041	G=0.3959
KOREAN population from KRGDB	KOREAN	Study-wide	2930	C=0.4628	G=0.5372
HapMap	Global	Study-wide	1604	C=0.6920	G=0.3080
HapMap	African	Sub	688	C=0.882	G=0.118
HapMap	American	Sub	486	C=0.564	G=0.436
HapMap	Asian	Sub	254	C=0.441	G=0.559
HapMap	Europe	Sub	176	C=0.665	G=0.335
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.612	G=0.388
Northern Sweden	ACPOP	Study-wide	600	C=0.587	G=0.413
SGDP_PRJ	Global	Study-wide	388	C=0.253	G=0.747
Qatari	Global	Study-wide	216	C=0.602	G=0.398
A Vietnamese Genetic Variation Database	Global	Study-wide	212	C=0.354	G=0.646
The Danish reference pan genome	Danish	Study-wide	40	C=0.57	G=0.42
Siberian	Global	Study-wide	32	C=0.28	G=0.72

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 15	NC_000015.10:g.22825366C>A
GRCh38.p14 chr 15	NC_000015.10:g.22825366C>G
GRCh37.p13 chr 15	NC_000015.9:g.23047702G>T
GRCh37.p13 chr 15	NC_000015.9:g.23047702G>C
NIPA1 RefSeqGene	NG_009056.1:g.44142C>A
NIPA1 RefSeqGene	NG_009056.1:g.44142C>G
GRCh38.p14 chr 15 fix patch HG2365_PATCH	NW_021160017.1:g.3719410C>A
GRCh38.p14 chr 15 fix patch HG2365_PATCH	NW_021160017.1:g.3719410C>G

Gene: NIPA1, NIPA magnesium transporter 1 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
NIPA1 transcript variant 2	NM_001142275.1:c.*1127=	N/A	3 Prime UTR Variant
NIPA1 transcript variant 1	NM_144599.5:c.*1127=	N/A	3 Prime UTR 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.

Allele: G (allele ID: 338164 )

ClinVar Accession	Disease Names	Clinical Significance
RCV000303318.3	Hereditary spastic paraplegia 6	Benign

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 15	NC_000015.10:g.22825366=	NC_000015.10:g.22825366C>A	NC_000015.10:g.22825366C>G
GRCh37.p13 chr 15	NC_000015.9:g.23047702=	NC_000015.9:g.23047702G>T	NC_000015.9:g.23047702G>C
NIPA1 RefSeqGene	NG_009056.1:g.44142=	NG_009056.1:g.44142C>A	NG_009056.1:g.44142C>G
NIPA1 transcript variant 1	NM_144599.5:c.*1127=	NM_144599.5:c.*1127C>A	NM_144599.5:c.*1127C>G
NIPA1 transcript variant 1	NM_144599.4:c.*1127=	NM_144599.4:c.*1127C>A	NM_144599.4:c.*1127C>G
NIPA1 transcript variant 2	NM_001142275.1:c.*1127=	NM_001142275.1:c.*1127C>A	NM_001142275.1:c.*1127C>G
GRCh38.p14 chr 15 fix patch HG2365_PATCH	NW_021160017.1:g.3719410=	NW_021160017.1:g.3719410C>A	NW_021160017.1:g.3719410C>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#.

80 SubSNP, 21 Frequency, 1 ClinVar submissions

No	Submitter	Submission ID	Date (Build)
1	LEE	ss1542677	Oct 05, 2000 (86)
2	CGAP-GAI	ss4322901	Jan 04, 2002 (102)
3	LEE	ss4399228	May 29, 2002 (106)
4	LEE	ss4429172	May 29, 2002 (106)
5	SSAHASNP	ss21237222	Apr 05, 2004 (121)
6	ABI	ss43782838	Mar 13, 2006 (126)
7	ILLUMINA	ss65732635	Oct 16, 2006 (127)
8	AFFY	ss66334793	Nov 29, 2006 (127)
9	AFFY	ss76034178	Dec 07, 2007 (129)
10	KRIBB_YJKIM	ss81453094	Dec 14, 2007 (130)
11	HUMANGENOME_JCVI	ss96742405	Feb 03, 2009 (130)
12	1000GENOMES	ss108662480	Jan 23, 2009 (130)
13	ENSEMBL	ss136941620	Dec 01, 2009 (131)
14	GMI	ss156306616	Dec 01, 2009 (131)
15	ILLUMINA	ss159911330	Dec 01, 2009 (131)
16	AFFY	ss170666977	Jul 04, 2010 (132)
17	COMPLETE_GENOMICS	ss170836633	Jul 04, 2010 (132)
18	1000GENOMES	ss226792063	Jul 14, 2010 (132)
19	1000GENOMES	ss236706744	Jul 15, 2010 (132)
20	1000GENOMES	ss243108503	Jul 15, 2010 (132)
21	GMI	ss282175203	May 04, 2012 (137)
22	PJP	ss291799255	May 09, 2011 (134)
23	ILLUMINA	ss479711197	Sep 08, 2015 (146)
24	ILLUMINA	ss536169209	Sep 08, 2015 (146)
25	SSMP	ss660065955	Apr 25, 2013 (138)
26	EVA-GONL	ss991579568	Aug 21, 2014 (142)
27	JMKIDD_LAB	ss1079971314	Aug 21, 2014 (142)
28	1000GENOMES	ss1352660472	Aug 21, 2014 (142)
29	DDI	ss1427560933	Apr 01, 2015 (144)
30	EVA_GENOME_DK	ss1577501538	Apr 01, 2015 (144)
31	EVA_UK10K_ALSPAC	ss1632594318	Apr 01, 2015 (144)
32	EVA_UK10K_TWINSUK	ss1675588351	Apr 01, 2015 (144)
33	EVA_DECODE	ss1695592088	Apr 01, 2015 (144)
34	EVA_SVP	ss1713474860	Apr 01, 2015 (144)
35	WEILL_CORNELL_DGM	ss1934972240	Feb 12, 2016 (147)
36	ILLUMINA	ss1959594086	Feb 12, 2016 (147)
37	GENOMED	ss1968060288	Jul 19, 2016 (147)
38	JJLAB	ss2028267952	Sep 14, 2016 (149)
39	USC_VALOUEV	ss2156663935	Dec 20, 2016 (150)
40	HUMAN_LONGEVITY	ss2205251057	Dec 20, 2016 (150)
41	SYSTEMSBIOZJU	ss2628625817	Nov 08, 2017 (151)
42	GRF	ss2701118317	Nov 08, 2017 (151)
43	GNOMAD	ss2932529451	Nov 08, 2017 (151)
44	SWEGEN	ss3012934431	Nov 08, 2017 (151)
45	ILLUMINA	ss3021612448	Nov 08, 2017 (151)
46	BIOINF_KMB_FNS_UNIBA	ss3027957759	Nov 08, 2017 (151)
47	CSHL	ss3351019053	Nov 08, 2017 (151)
48	ILLUMINA	ss3627314858	Oct 12, 2018 (152)
49	ILLUMINA	ss3636286131	Oct 12, 2018 (152)
50	OMUKHERJEE_ADBS	ss3646468609	Oct 12, 2018 (152)
51	URBANLAB	ss3650305426	Oct 12, 2018 (152)
52	ILLUMINA	ss3652011589	Oct 12, 2018 (152)
53	EGCUT_WGS	ss3680122087	Jul 13, 2019 (153)
54	EVA_DECODE	ss3697503954	Jul 13, 2019 (153)
55	ILLUMINA	ss3725481501	Jul 13, 2019 (153)
56	ACPOP	ss3740749223	Jul 13, 2019 (153)
57	EVA	ss3752840977	Jul 13, 2019 (153)
58	PAGE_CC	ss3771816217	Jul 13, 2019 (153)
59	KHV_HUMAN_GENOMES	ss3818155293	Jul 13, 2019 (153)
60	EVA	ss3825854341	Apr 27, 2020 (154)
61	EVA	ss3834134784	Apr 27, 2020 (154)
62	EVA	ss3840661415	Apr 27, 2020 (154)
63	EVA	ss3846149942	Apr 27, 2020 (154)
64	SGDP_PRJ	ss3882456081	Apr 27, 2020 (154)
65	KRGDB	ss3931576372	Apr 27, 2020 (154)
66	FSA-LAB	ss3984067600	Apr 26, 2021 (155)
67	EVA	ss3986066240	Apr 26, 2021 (155)
68	TOPMED	ss4984396729	Apr 26, 2021 (155)
69	TOMMO_GENOMICS	ss5215211681	Apr 26, 2021 (155)
70	1000G_HIGH_COVERAGE	ss5297709205	Oct 16, 2022 (156)
71	EVA	ss5417943328	Oct 16, 2022 (156)
72	HUGCELL_USP	ss5491549070	Oct 16, 2022 (156)
73	1000G_HIGH_COVERAGE	ss5598750265	Oct 16, 2022 (156)
74	SANFORD_IMAGENETICS	ss5657083516	Oct 16, 2022 (156)
75	TOMMO_GENOMICS	ss5768732368	Oct 16, 2022 (156)
76	YY_MCH	ss5815147061	Oct 16, 2022 (156)
77	EVA	ss5827924438	Oct 16, 2022 (156)
78	EVA	ss5851208872	Oct 16, 2022 (156)
79	EVA	ss5875090188	Oct 16, 2022 (156)
80	EVA	ss5948502541	Oct 16, 2022 (156)
81	1000Genomes	NC_000015.9 - 23047702	Oct 12, 2018 (152)
82	1000Genomes_30x	NC_000015.10 - 22825366	Oct 16, 2022 (156)
83	The Avon Longitudinal Study of Parents and Children	NC_000015.9 - 23047702	Oct 12, 2018 (152)
84	Genetic variation in the Estonian population	NC_000015.9 - 23047702	Oct 12, 2018 (152)
85	The Danish reference pan genome	NC_000015.9 - 23047702	Apr 27, 2020 (154)
86	gnomAD - Genomes Submission ignored due to conflicting rows: Row 463143922 (NC_000015.10:22825365:C:A 0/140094) Row 463143923 (NC_000015.10:22825365:C:G 46939/140040)	-	Apr 26, 2021 (155)
87	gnomAD - Genomes Submission ignored due to conflicting rows: Row 463143922 (NC_000015.10:22825365:C:A 0/140094) Row 463143923 (NC_000015.10:22825365:C:G 46939/140040)	-	Apr 26, 2021 (155)
88	Genome of the Netherlands Release 5	NC_000015.9 - 23047702	Apr 27, 2020 (154)
89	HapMap	NC_000015.10 - 22825366	Apr 27, 2020 (154)
90	KOREAN population from KRGDB	NC_000015.9 - 23047702	Apr 27, 2020 (154)
91	Northern Sweden	NC_000015.9 - 23047702	Jul 13, 2019 (153)
92	The PAGE Study	NC_000015.10 - 22825366	Jul 13, 2019 (153)
93	Qatari	NC_000015.9 - 23047702	Apr 27, 2020 (154)
94	SGDP_PRJ	NC_000015.9 - 23047702	Apr 27, 2020 (154)
95	Siberian	NC_000015.9 - 23047702	Apr 27, 2020 (154)
96	8.3KJPN	NC_000015.9 - 23047702	Apr 26, 2021 (155)
97	14KJPN	NC_000015.10 - 22825366	Oct 16, 2022 (156)
98	TopMed	NC_000015.10 - 22825366	Apr 26, 2021 (155)
99	UK 10K study - Twins	NC_000015.9 - 23047702	Oct 12, 2018 (152)
100	A Vietnamese Genetic Variation Database	NC_000015.9 - 23047702	Jul 13, 2019 (153)
101	ALFA	NC_000015.10 - 22825366	Apr 26, 2021 (155)
102	ClinVar	RCV000303318.3	Oct 16, 2022 (156)

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)
rs3169172	Jul 03, 2002 (106)
rs56924204	Feb 26, 2009 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
363518164	NC_000015.10:22825365:C:A	NC_000015.10:22825365:C:A	(self)
ss66334793, ss76034178, ss108662480, ss159911330, ss170666977, ss170836633, ss282175203, ss291799255, ss1695592088, ss1713474860	NC_000015.8:20599142:G:C	NC_000015.10:22825365:C:G	(self)
65701611, 36490103, 25860335, 3775510, 16294859, 38753766, 14034088, 17014170, 34473061, 9180289, 73180988, 36490103, 8117765, ss226792063, ss236706744, ss243108503, ss479711197, ss536169209, ss660065955, ss991579568, ss1079971314, ss1352660472, ss1427560933, ss1577501538, ss1632594318, ss1675588351, ss1934972240, ss1959594086, ss1968060288, ss2028267952, ss2156663935, ss2628625817, ss2701118317, ss2932529451, ss3012934431, ss3021612448, ss3351019053, ss3627314858, ss3636286131, ss3646468609, ss3652011589, ss3680122087, ss3740749223, ss3752840977, ss3825854341, ss3834134784, ss3840661415, ss3882456081, ss3931576372, ss3984067600, ss3986066240, ss5215211681, ss5417943328, ss5657083516, ss5827924438, ss5948502541	NC_000015.9:23047701:G:C	NC_000015.10:22825365:C:G	(self)
RCV000303318.3, 86276200, 1225073, 1037686, 102569472, 199942389, 363518164, ss2205251057, ss3027957759, ss3650305426, ss3697503954, ss3725481501, ss3771816217, ss3818155293, ss3846149942, ss4984396729, ss5297709205, ss5491549070, ss5598750265, ss5768732368, ss5815147061, ss5851208872, ss5875090188	NC_000015.10:22825365:C:G	NC_000015.10:22825365:C:G	(self)
ss21237222	NT_078094.1:401585:G:C	NC_000015.10:22825365:C:G	(self)
ss1542677, ss4322901, ss4399228, ss4429172, ss43782838, ss65732635, ss81453094, ss96742405, ss136941620, ss156306616	NT_078094.2:401508:G:C	NC_000015.10:22825365: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 rs1059774

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

rs1059774