Name: rs62064886
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.

rs62064886

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr17:4469883 (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: T=0.185387 (49070/264690, TOPMED)
T=0.190726 (26644/139698, GnomAD)
T=0.13753 (10824/78700, PAGE_STUDY) (+ 17 more)
T=0.08376 (2367/28258, 14KJPN)
T=0.19703 (3677/18662, ALFA)
T=0.08508 (1426/16760, 8.3KJPN)
T=0.1405 (900/6404, 1000G_30x)
T=0.1408 (705/5008, 1000G)
T=0.1897 (850/4480, Estonian)
T=0.2423 (934/3854, ALSPAC)
T=0.2505 (929/3708, TWINSUK)
T=0.0561 (164/2922, KOREAN)
T=0.0486 (89/1832, Korea1K)
T=0.247 (247/998, GoNL)
T=0.213 (128/600, NorthernSweden)
T=0.264 (57/216, Qatari)
T=0.028 (6/216, Vietnamese)
C=0.421 (59/140, SGDP_PRJ)
T=0.17 (7/40, GENOME_DK)
C=0.46 (11/24, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: SPNS3 : 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	18662	C=0.80297	A=0.00000, T=0.19703
European	Sub	14056	C=0.77540	A=0.00000, T=0.22460
African	Sub	2854	C=0.9247	A=0.0000, T=0.0753
African Others	Sub	112	C=0.946	A=0.000, T=0.054
African American	Sub	2742	C=0.9238	A=0.0000, T=0.0762
Asian	Sub	146	C=0.904	A=0.000, T=0.096
East Asian	Sub	120	C=0.917	A=0.000, T=0.083
Other Asian	Sub	26	C=0.85	A=0.00, T=0.15
Latin American 1	Sub	146	C=0.767	A=0.000, T=0.233
Latin American 2	Sub	610	C=0.826	A=0.000, T=0.174
South Asian	Sub	104	C=0.817	A=0.000, T=0.183
Other	Sub	746	C=0.823	A=0.000, T=0.177

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").

Download

Study	Population	Group	Sample Size	Ref Allele	Alt Allele
TopMed	Global	Study-wide	264690	C=0.814613	T=0.185387
gnomAD - Genomes	Global	Study-wide	139698	C=0.809274	T=0.190726
gnomAD - Genomes	European	Sub	75702	C=0.75665	T=0.24335
gnomAD - Genomes	African	Sub	41848	C=0.90368	T=0.09632
gnomAD - Genomes	American	Sub	13570	C=0.79764	T=0.20236
gnomAD - Genomes	Ashkenazi Jewish	Sub	3318	C=0.7553	T=0.2447
gnomAD - Genomes	East Asian	Sub	3124	C=0.9385	T=0.0615
gnomAD - Genomes	Other	Sub	2136	C=0.7935	T=0.2065
The PAGE Study	Global	Study-wide	78700	C=0.86247	T=0.13753
The PAGE Study	AfricanAmerican	Sub	32514	C=0.90358	T=0.09642
The PAGE Study	Mexican	Sub	10810	C=0.83145	T=0.16855
The PAGE Study	Asian	Sub	8318	C=0.9207	T=0.0793
The PAGE Study	PuertoRican	Sub	7918	C=0.7905	T=0.2095
The PAGE Study	NativeHawaiian	Sub	4534	C=0.8262	T=0.1738
The PAGE Study	Cuban	Sub	4230	C=0.7657	T=0.2343
The PAGE Study	Dominican	Sub	3828	C=0.8268	T=0.1732
The PAGE Study	CentralAmerican	Sub	2450	C=0.8531	T=0.1469
The PAGE Study	SouthAmerican	Sub	1982	C=0.8416	T=0.1584
The PAGE Study	NativeAmerican	Sub	1260	C=0.7762	T=0.2238
The PAGE Study	SouthAsian	Sub	856	C=0.825	T=0.175
14KJPN	JAPANESE	Study-wide	28258	C=0.91624	T=0.08376
Allele Frequency Aggregator	Total	Global	18662	C=0.80297	A=0.00000, T=0.19703
Allele Frequency Aggregator	European	Sub	14056	C=0.77540	A=0.00000, T=0.22460
Allele Frequency Aggregator	African	Sub	2854	C=0.9247	A=0.0000, T=0.0753
Allele Frequency Aggregator	Other	Sub	746	C=0.823	A=0.000, T=0.177
Allele Frequency Aggregator	Latin American 2	Sub	610	C=0.826	A=0.000, T=0.174
Allele Frequency Aggregator	Latin American 1	Sub	146	C=0.767	A=0.000, T=0.233
Allele Frequency Aggregator	Asian	Sub	146	C=0.904	A=0.000, T=0.096
Allele Frequency Aggregator	South Asian	Sub	104	C=0.817	A=0.000, T=0.183
8.3KJPN	JAPANESE	Study-wide	16760	C=0.91492	T=0.08508
1000Genomes_30x	Global	Study-wide	6404	C=0.8595	T=0.1405
1000Genomes_30x	African	Sub	1786	C=0.9462	T=0.0538
1000Genomes_30x	Europe	Sub	1266	C=0.7393	T=0.2607
1000Genomes_30x	South Asian	Sub	1202	C=0.8120	T=0.1880
1000Genomes_30x	East Asian	Sub	1170	C=0.9316	T=0.0684
1000Genomes_30x	American	Sub	980	C=0.829	T=0.171
1000Genomes	Global	Study-wide	5008	C=0.8592	T=0.1408
1000Genomes	African	Sub	1322	C=0.9448	T=0.0552
1000Genomes	East Asian	Sub	1008	C=0.9286	T=0.0714
1000Genomes	Europe	Sub	1006	C=0.7465	T=0.2535
1000Genomes	South Asian	Sub	978	C=0.809	T=0.191
1000Genomes	American	Sub	694	C=0.830	T=0.170
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.8103	T=0.1897
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.7577	T=0.2423
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.7495	T=0.2505
KOREAN population from KRGDB	KOREAN	Study-wide	2922	C=0.9439	T=0.0561
Korean Genome Project	KOREAN	Study-wide	1832	C=0.9514	T=0.0486
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.753	T=0.247
Northern Sweden	ACPOP	Study-wide	600	C=0.787	T=0.213
Qatari	Global	Study-wide	216	C=0.736	T=0.264
A Vietnamese Genetic Variation Database	Global	Study-wide	216	C=0.972	T=0.028
SGDP_PRJ	Global	Study-wide	140	C=0.421	T=0.579
The Danish reference pan genome	Danish	Study-wide	40	C=0.82	T=0.17
Siberian	Global	Study-wide	24	C=0.46	T=0.54

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 17	NC_000017.11:g.4469883C>A
GRCh38.p14 chr 17	NC_000017.11:g.4469883C>T
GRCh37.p13 chr 17	NC_000017.10:g.4373178C>A
GRCh37.p13 chr 17	NC_000017.10:g.4373178C>T

Gene: SPNS3, sphingolipid transporter 3 (putative) (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
SPNS3 transcript variant 2	NM_001320449.2:c.733-8689… NM_001320449.2:c.733-8689C>A	N/A	Intron Variant
SPNS3 transcript variant 1	NM_182538.5:c.1114-8689C>A	N/A	Intron Variant
SPNS3 transcript variant X1	XM_011523723.1:c.1114-163… XM_011523723.1:c.1114-16345C>A	N/A	Intron Variant
SPNS3 transcript variant X2	XM_011523724.1:c.1114-868… XM_011523724.1:c.1114-8689C>A	N/A	Intron Variant
SPNS3 transcript variant X3	XM_011523725.1:c.961-8689… XM_011523725.1:c.961-8689C>A	N/A	Intron Variant
SPNS3 transcript variant X7	XM_011523728.3:c.526-8689… XM_011523728.3:c.526-8689C>A	N/A	Intron Variant
SPNS3 transcript variant X8	XM_017024345.3:c.388-8689… XM_017024345.3:c.388-8689C>A	N/A	Intron Variant
SPNS3 transcript variant X5	XM_047435588.1:c.775-8689… XM_047435588.1:c.775-8689C>A	N/A	Intron Variant
SPNS3 transcript variant X6	XM_047435589.1:c.	N/A	Genic Downstream Transcript Variant
SPNS3 transcript variant X4	XR_934008.1: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	T
GRCh38.p14 chr 17	NC_000017.11:g.4469883=	NC_000017.11:g.4469883C>A	NC_000017.11:g.4469883C>T
GRCh37.p13 chr 17	NC_000017.10:g.4373178=	NC_000017.10:g.4373178C>A	NC_000017.10:g.4373178C>T
SPNS3 transcript variant 2	NM_001320449.2:c.733-8689=	NM_001320449.2:c.733-8689C>A	NM_001320449.2:c.733-8689C>T
SPNS3 transcript variant 1	NM_182538.4:c.1114-8689=	NM_182538.4:c.1114-8689C>A	NM_182538.4:c.1114-8689C>T
SPNS3 transcript variant 1	NM_182538.5:c.1114-8689=	NM_182538.5:c.1114-8689C>A	NM_182538.5:c.1114-8689C>T
SPNS3 transcript variant X1	XM_005256520.1:c.733-8689=	XM_005256520.1:c.733-8689C>A	XM_005256520.1:c.733-8689C>T
SPNS3 transcript variant X1	XM_011523723.1:c.1114-16345=	XM_011523723.1:c.1114-16345C>A	XM_011523723.1:c.1114-16345C>T
SPNS3 transcript variant X2	XM_011523724.1:c.1114-8689=	XM_011523724.1:c.1114-8689C>A	XM_011523724.1:c.1114-8689C>T
SPNS3 transcript variant X3	XM_011523725.1:c.961-8689=	XM_011523725.1:c.961-8689C>A	XM_011523725.1:c.961-8689C>T
SPNS3 transcript variant X7	XM_011523728.3:c.526-8689=	XM_011523728.3:c.526-8689C>A	XM_011523728.3:c.526-8689C>T
SPNS3 transcript variant X8	XM_017024345.3:c.388-8689=	XM_017024345.3:c.388-8689C>A	XM_017024345.3:c.388-8689C>T
SPNS3 transcript variant X5	XM_047435588.1:c.775-8689=	XM_047435588.1:c.775-8689C>A	XM_047435588.1:c.775-8689C>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#.

60 SubSNP, 20 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	BCMHGSC_JDW	ss90515325	Mar 24, 2008 (129)
2	ENSEMBL	ss136949061	Dec 01, 2009 (131)
3	GMI	ss157779398	Dec 01, 2009 (131)
4	COMPLETE_GENOMICS	ss171093909	Jul 04, 2010 (132)
5	1000GENOMES	ss237164075	Jul 15, 2010 (132)
6	1000GENOMES	ss243477769	Jul 15, 2010 (132)
7	GMI	ss282672213	May 04, 2012 (137)
8	TISHKOFF	ss565136109	Apr 25, 2013 (138)
9	SSMP	ss660922930	Apr 25, 2013 (138)
10	EVA-GONL	ss992872208	Aug 21, 2014 (142)
11	JMKIDD_LAB	ss1080896072	Aug 21, 2014 (142)
12	1000GENOMES	ss1357714109	Aug 21, 2014 (142)
13	DDI	ss1427961541	Apr 01, 2015 (144)
14	EVA_GENOME_DK	ss1578067828	Apr 01, 2015 (144)
15	EVA_UK10K_ALSPAC	ss1635188776	Apr 01, 2015 (144)
16	EVA_UK10K_TWINSUK	ss1678182809	Apr 01, 2015 (144)
17	EVA_DECODE	ss1696912686	Apr 01, 2015 (144)
18	WEILL_CORNELL_DGM	ss1936318473	Feb 12, 2016 (147)
19	ILLUMINA	ss1959716759	Feb 12, 2016 (147)
20	JJLAB	ss2028947175	Sep 14, 2016 (149)
21	USC_VALOUEV	ss2157392759	Dec 20, 2016 (150)
22	HUMAN_LONGEVITY	ss2215121866	Dec 20, 2016 (150)
23	GRF	ss2701934328	Nov 08, 2017 (151)
24	GNOMAD	ss2947154817	Nov 08, 2017 (151)
25	SWEGEN	ss3015113760	Nov 08, 2017 (151)
26	ILLUMINA	ss3021747740	Nov 08, 2017 (151)
27	BIOINF_KMB_FNS_UNIBA	ss3028291977	Nov 08, 2017 (151)
28	CSHL	ss3351629048	Nov 08, 2017 (151)
29	ILLUMINA	ss3652160355	Oct 12, 2018 (152)
30	EGCUT_WGS	ss3682081167	Jul 13, 2019 (153)
31	EVA_DECODE	ss3699986294	Jul 13, 2019 (153)
32	ILLUMINA	ss3725596082	Jul 13, 2019 (153)
33	ACPOP	ss3741828897	Jul 13, 2019 (153)
34	EVA	ss3754390558	Jul 13, 2019 (153)
35	PAGE_CC	ss3771907464	Jul 13, 2019 (153)
36	KHV_HUMAN_GENOMES	ss3819660039	Jul 13, 2019 (153)
37	EVA	ss3834752853	Apr 27, 2020 (154)
38	EVA	ss3840984688	Apr 27, 2020 (154)
39	EVA	ss3846478899	Apr 27, 2020 (154)
40	SGDP_PRJ	ss3885235615	Apr 27, 2020 (154)
41	KRGDB	ss3934819366	Apr 27, 2020 (154)
42	KOGIC	ss3978297224	Apr 27, 2020 (154)
43	TOPMED	ss5027844089	Apr 26, 2021 (155)
44	TOMMO_GENOMICS	ss5221269159	Apr 26, 2021 (155)
45	EVA	ss5237571110	Apr 26, 2021 (155)
46	1000G_HIGH_COVERAGE	ss5302254107	Oct 16, 2022 (156)
47	EVA	ss5426081113	Oct 16, 2022 (156)
48	HUGCELL_USP	ss5495447541	Oct 16, 2022 (156)
49	1000G_HIGH_COVERAGE	ss5605531714	Oct 16, 2022 (156)
50	SANFORD_IMAGENETICS	ss5624390756	Oct 16, 2022 (156)
51	SANFORD_IMAGENETICS	ss5659626465	Oct 16, 2022 (156)
52	TOMMO_GENOMICS	ss5776795163	Oct 16, 2022 (156)
53	YY_MCH	ss5816292493	Oct 16, 2022 (156)
54	EVA	ss5833652928	Oct 16, 2022 (156)
55	EVA	ss5847470147	Oct 16, 2022 (156)
56	EVA	ss5847785905	Oct 16, 2022 (156)
57	EVA	ss5851717751	Oct 16, 2022 (156)
58	EVA	ss5913034883	Oct 16, 2022 (156)
59	EVA	ss5951035465	Oct 16, 2022 (156)
60	EVA	ss5979498167	Oct 16, 2022 (156)
61	1000Genomes	NC_000017.10 - 4373178	Oct 12, 2018 (152)
62	1000Genomes_30x	NC_000017.11 - 4469883	Oct 16, 2022 (156)
63	The Avon Longitudinal Study of Parents and Children	NC_000017.10 - 4373178	Oct 12, 2018 (152)
64	Genetic variation in the Estonian population	NC_000017.10 - 4373178	Oct 12, 2018 (152)
65	The Danish reference pan genome	NC_000017.10 - 4373178	Apr 27, 2020 (154)
66	gnomAD - Genomes	NC_000017.11 - 4469883	Apr 26, 2021 (155)
67	Genome of the Netherlands Release 5	NC_000017.10 - 4373178	Apr 27, 2020 (154)
68	KOREAN population from KRGDB	NC_000017.10 - 4373178	Apr 27, 2020 (154)
69	Korean Genome Project	NC_000017.11 - 4469883	Apr 27, 2020 (154)
70	Northern Sweden	NC_000017.10 - 4373178	Jul 13, 2019 (153)
71	The PAGE Study	NC_000017.11 - 4469883	Jul 13, 2019 (153)
72	Qatari	NC_000017.10 - 4373178	Apr 27, 2020 (154)
73	SGDP_PRJ	NC_000017.10 - 4373178	Apr 27, 2020 (154)
74	Siberian	NC_000017.10 - 4373178	Apr 27, 2020 (154)
75	8.3KJPN	NC_000017.10 - 4373178	Apr 26, 2021 (155)
76	14KJPN	NC_000017.11 - 4469883	Oct 16, 2022 (156)
77	TopMed	NC_000017.11 - 4469883	Apr 26, 2021 (155)
78	UK 10K study - Twins	NC_000017.10 - 4373178	Oct 12, 2018 (152)
79	A Vietnamese Genetic Variation Database	NC_000017.10 - 4373178	Jul 13, 2019 (153)
80	ALFA	NC_000017.11 - 4469883	Apr 26, 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
1949610269	NC_000017.11:4469882:C:A	NC_000017.11:4469882:C:A	(self)
ss90515325, ss171093909, ss282672213, ss1696912686	NC_000017.9:4319926:C:T	NC_000017.11:4469882:C:T	(self)
70920892, 39333254, 27819415, 4273726, 17535648, 41996760, 15113762, 18360395, 37252595, 9909113, 79238466, 39333254, 8713953, ss237164075, ss243477769, ss565136109, ss660922930, ss992872208, ss1080896072, ss1357714109, ss1427961541, ss1578067828, ss1635188776, ss1678182809, ss1936318473, ss1959716759, ss2028947175, ss2157392759, ss2701934328, ss2947154817, ss3015113760, ss3021747740, ss3351629048, ss3652160355, ss3682081167, ss3741828897, ss3754390558, ss3834752853, ss3840984688, ss3885235615, ss3934819366, ss5221269159, ss5237571110, ss5426081113, ss5624390756, ss5659626465, ss5833652928, ss5847470147, ss5847785905, ss5951035465, ss5979498167	NC_000017.10:4373177:C:T	NC_000017.11:4469882:C:T	(self)
93057649, 500107883, 34675225, 1128933, 110632267, 243389751, 1949610269, ss2215121866, ss3028291977, ss3699986294, ss3725596082, ss3771907464, ss3819660039, ss3846478899, ss3978297224, ss5027844089, ss5302254107, ss5495447541, ss5605531714, ss5776795163, ss5816292493, ss5851717751, ss5913034883	NC_000017.11:4469882:C:T	NC_000017.11:4469882:C:T	(self)
ss136949061, ss157779398	NT_010718.16:3976551:C:T	NC_000017.11:4469882: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 rs62064886

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

rs62064886