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dbSNP Short Genetic Variations

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.

rs62064884

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr17:4468352 (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>C
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.161453 (42735/264690, TOPMED)
C=0.162483 (22771/140144, GnomAD)
C=0.16271 (5022/30864, ALFA) (+ 16 more)
C=0.04897 (1380/28180, 14KJPN)
C=0.05054 (847/16760, 8.3KJPN)
C=0.1410 (903/6404, 1000G_30x)
C=0.1388 (695/5008, 1000G)
C=0.1317 (590/4480, Estonian)
C=0.1510 (582/3854, ALSPAC)
C=0.1648 (611/3708, TWINSUK)
C=0.0500 (146/2922, KOREAN)
C=0.0404 (74/1832, Korea1K)
C=0.158 (158/998, GoNL)
C=0.113 (68/600, NorthernSweden)
C=0.190 (41/216, Qatari)
C=0.024 (5/212, Vietnamese)
A=0.426 (52/122, SGDP_PRJ)
C=0.12 (5/40, GENOME_DK)
A=0.45 (9/20, 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 30864 A=0.83729 C=0.16271
European Sub 24734 A=0.83759 C=0.16241
African Sub 3168 A=0.8267 C=0.1733
African Others Sub 124 A=0.823 C=0.177
African American Sub 3044 A=0.8269 C=0.1731
Asian Sub 128 A=0.914 C=0.086
East Asian Sub 100 A=0.92 C=0.08
Other Asian Sub 28 A=0.89 C=0.11
Latin American 1 Sub 168 A=0.839 C=0.161
Latin American 2 Sub 700 A=0.851 C=0.149
South Asian Sub 114 A=0.842 C=0.158
Other Sub 1852 A=0.8402 C=0.1598


Help

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 A=0.838547 C=0.161453
gnomAD - Genomes Global Study-wide 140144 A=0.837517 C=0.162483
gnomAD - Genomes European Sub 75900 A=0.83563 C=0.16437
gnomAD - Genomes African Sub 42008 A=0.82856 C=0.17144
gnomAD - Genomes American Sub 13632 A=0.84602 C=0.15398
gnomAD - Genomes Ashkenazi Jewish Sub 3320 A=0.8370 C=0.1630
gnomAD - Genomes East Asian Sub 3132 A=0.9652 C=0.0348
gnomAD - Genomes Other Sub 2152 A=0.8401 C=0.1599
Allele Frequency Aggregator Total Global 30864 A=0.83729 C=0.16271
Allele Frequency Aggregator European Sub 24734 A=0.83759 C=0.16241
Allele Frequency Aggregator African Sub 3168 A=0.8267 C=0.1733
Allele Frequency Aggregator Other Sub 1852 A=0.8402 C=0.1598
Allele Frequency Aggregator Latin American 2 Sub 700 A=0.851 C=0.149
Allele Frequency Aggregator Latin American 1 Sub 168 A=0.839 C=0.161
Allele Frequency Aggregator Asian Sub 128 A=0.914 C=0.086
Allele Frequency Aggregator South Asian Sub 114 A=0.842 C=0.158
14KJPN JAPANESE Study-wide 28180 A=0.95103 C=0.04897
8.3KJPN JAPANESE Study-wide 16760 A=0.94946 C=0.05054
1000Genomes_30x Global Study-wide 6404 A=0.8590 C=0.1410
1000Genomes_30x African Sub 1786 A=0.8180 C=0.1820
1000Genomes_30x Europe Sub 1266 A=0.8278 C=0.1722
1000Genomes_30x South Asian Sub 1202 A=0.8511 C=0.1489
1000Genomes_30x East Asian Sub 1170 A=0.9564 C=0.0436
1000Genomes_30x American Sub 980 A=0.867 C=0.133
1000Genomes Global Study-wide 5008 A=0.8612 C=0.1388
1000Genomes African Sub 1322 A=0.8222 C=0.1778
1000Genomes East Asian Sub 1008 A=0.9534 C=0.0466
1000Genomes Europe Sub 1006 A=0.8310 C=0.1690
1000Genomes South Asian Sub 978 A=0.849 C=0.151
1000Genomes American Sub 694 A=0.863 C=0.137
Genetic variation in the Estonian population Estonian Study-wide 4480 A=0.8683 C=0.1317
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.8490 C=0.1510
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.8352 C=0.1648
KOREAN population from KRGDB KOREAN Study-wide 2922 A=0.9500 C=0.0500
Korean Genome Project KOREAN Study-wide 1832 A=0.9596 C=0.0404
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 A=0.842 C=0.158
Northern Sweden ACPOP Study-wide 600 A=0.887 C=0.113
Qatari Global Study-wide 216 A=0.810 C=0.190
A Vietnamese Genetic Variation Database Global Study-wide 212 A=0.976 C=0.024
SGDP_PRJ Global Study-wide 122 A=0.426 C=0.574
The Danish reference pan genome Danish Study-wide 40 A=0.88 C=0.12
Siberian Global Study-wide 20 A=0.45 C=0.55
Help

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.4468352A>C
GRCh37.p13 chr 17 NC_000017.10:g.4371647A>C
Gene: SPNS3, sphingolipid transporter 3 (putative) (plus strand)
Molecule type Change Amino acid[Codon] SO Term
SPNS3 transcript variant 2 NM_001320449.2:c.733-1022…

NM_001320449.2:c.733-10220A>C

N/A Intron Variant
SPNS3 transcript variant 1 NM_182538.5:c.1114-10220A…

NM_182538.5:c.1114-10220A>C

N/A Intron Variant
SPNS3 transcript variant X1 XM_011523723.1:c.1113+151…

XM_011523723.1:c.1113+15147A>C

N/A Intron Variant
SPNS3 transcript variant X2 XM_011523724.1:c.1114-102…

XM_011523724.1:c.1114-10220A>C

N/A Intron Variant
SPNS3 transcript variant X3 XM_011523725.1:c.961-1022…

XM_011523725.1:c.961-10220A>C

N/A Intron Variant
SPNS3 transcript variant X7 XM_011523728.3:c.526-1022…

XM_011523728.3:c.526-10220A>C

N/A Intron Variant
SPNS3 transcript variant X8 XM_017024345.3:c.388-1022…

XM_017024345.3:c.388-10220A>C

N/A Intron Variant
SPNS3 transcript variant X5 XM_047435588.1:c.775-1022…

XM_047435588.1:c.775-10220A>C

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
Help

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
Help

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= C
GRCh38.p14 chr 17 NC_000017.11:g.4468352= NC_000017.11:g.4468352A>C
GRCh37.p13 chr 17 NC_000017.10:g.4371647= NC_000017.10:g.4371647A>C
SPNS3 transcript variant 2 NM_001320449.2:c.733-10220= NM_001320449.2:c.733-10220A>C
SPNS3 transcript variant 1 NM_182538.4:c.1114-10220= NM_182538.4:c.1114-10220A>C
SPNS3 transcript variant 1 NM_182538.5:c.1114-10220= NM_182538.5:c.1114-10220A>C
SPNS3 transcript variant X1 XM_005256520.1:c.733-10220= XM_005256520.1:c.733-10220A>C
SPNS3 transcript variant X1 XM_011523723.1:c.1113+15147= XM_011523723.1:c.1113+15147A>C
SPNS3 transcript variant X2 XM_011523724.1:c.1114-10220= XM_011523724.1:c.1114-10220A>C
SPNS3 transcript variant X3 XM_011523725.1:c.961-10220= XM_011523725.1:c.961-10220A>C
SPNS3 transcript variant X7 XM_011523728.3:c.526-10220= XM_011523728.3:c.526-10220A>C
SPNS3 transcript variant X8 XM_017024345.3:c.388-10220= XM_017024345.3:c.388-10220A>C
SPNS3 transcript variant X5 XM_047435588.1:c.775-10220= XM_047435588.1:c.775-10220A>C
Help

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#.

62 SubSNP, 19 Frequency submissions
No Submitter Submission ID Date (Build)
1 BCMHGSC_JDW ss90515315 Mar 24, 2008 (129)
2 ENSEMBL ss136949046 Dec 01, 2009 (131)
3 GMI ss157779366 Dec 01, 2009 (131)
4 COMPLETE_GENOMICS ss167693467 Jul 04, 2010 (132)
5 1000GENOMES ss227436971 Jul 14, 2010 (132)
6 1000GENOMES ss237164066 Jul 15, 2010 (132)
7 1000GENOMES ss243477764 Jul 15, 2010 (132)
8 GMI ss282672204 May 04, 2012 (137)
9 ILLUMINA ss482625919 May 04, 2012 (137)
10 ILLUMINA ss483631259 May 04, 2012 (137)
11 ILLUMINA ss534726050 Sep 08, 2015 (146)
12 TISHKOFF ss565136101 Apr 25, 2013 (138)
13 SSMP ss660922914 Apr 25, 2013 (138)
14 ILLUMINA ss780039130 Sep 08, 2015 (146)
15 ILLUMINA ss781823780 Sep 08, 2015 (146)
16 ILLUMINA ss835519616 Sep 08, 2015 (146)
17 EVA-GONL ss992872192 Aug 21, 2014 (142)
18 JMKIDD_LAB ss1080896059 Aug 21, 2014 (142)
19 1000GENOMES ss1357714064 Aug 21, 2014 (142)
20 DDI ss1427961534 Apr 01, 2015 (144)
21 EVA_GENOME_DK ss1578067816 Apr 01, 2015 (144)
22 EVA_UK10K_ALSPAC ss1635188750 Apr 01, 2015 (144)
23 EVA_UK10K_TWINSUK ss1678182783 Apr 01, 2015 (144)
24 EVA_DECODE ss1696912667 Apr 01, 2015 (144)
25 WEILL_CORNELL_DGM ss1936318450 Feb 12, 2016 (147)
26 JJLAB ss2028947166 Sep 14, 2016 (149)
27 USC_VALOUEV ss2157392744 Dec 20, 2016 (150)
28 HUMAN_LONGEVITY ss2215121757 Dec 20, 2016 (150)
29 ILLUMINA ss2633368466 Nov 08, 2017 (151)
30 GRF ss2701934309 Nov 08, 2017 (151)
31 GNOMAD ss2947154639 Nov 08, 2017 (151)
32 SWEGEN ss3015113715 Nov 08, 2017 (151)
33 BIOINF_KMB_FNS_UNIBA ss3028291970 Nov 08, 2017 (151)
34 CSHL ss3351629035 Nov 08, 2017 (151)
35 ILLUMINA ss3627612429 Oct 12, 2018 (152)
36 ILLUMINA ss3631351386 Oct 12, 2018 (152)
37 ILLUMINA ss3641980288 Oct 12, 2018 (152)
38 EGCUT_WGS ss3682081140 Jul 13, 2019 (153)
39 EVA_DECODE ss3699986264 Jul 13, 2019 (153)
40 ACPOP ss3741828877 Jul 13, 2019 (153)
41 EVA ss3754390541 Jul 13, 2019 (153)
42 KHV_HUMAN_GENOMES ss3819660023 Jul 13, 2019 (153)
43 EVA ss3834752842 Apr 27, 2020 (154)
44 EVA ss3840984678 Apr 27, 2020 (154)
45 EVA ss3846478890 Apr 27, 2020 (154)
46 SGDP_PRJ ss3885235570 Apr 27, 2020 (154)
47 KRGDB ss3934819308 Apr 27, 2020 (154)
48 KOGIC ss3978297188 Apr 27, 2020 (154)
49 TOPMED ss5027843679 Apr 26, 2021 (155)
50 TOMMO_GENOMICS ss5221269073 Apr 26, 2021 (155)
51 1000G_HIGH_COVERAGE ss5302254033 Oct 16, 2022 (156)
52 EVA ss5315869277 Oct 16, 2022 (156)
53 EVA ss5426081042 Oct 16, 2022 (156)
54 HUGCELL_USP ss5495447462 Oct 16, 2022 (156)
55 1000G_HIGH_COVERAGE ss5605531646 Oct 16, 2022 (156)
56 SANFORD_IMAGENETICS ss5659626430 Oct 16, 2022 (156)
57 TOMMO_GENOMICS ss5776795044 Oct 16, 2022 (156)
58 YY_MCH ss5816292473 Oct 16, 2022 (156)
59 EVA ss5833652901 Oct 16, 2022 (156)
60 EVA ss5851717743 Oct 16, 2022 (156)
61 EVA ss5913034831 Oct 16, 2022 (156)
62 EVA ss5951035437 Oct 16, 2022 (156)
63 1000Genomes NC_000017.10 - 4371647 Oct 12, 2018 (152)
64 1000Genomes_30x NC_000017.11 - 4468352 Oct 16, 2022 (156)
65 The Avon Longitudinal Study of Parents and Children NC_000017.10 - 4371647 Oct 12, 2018 (152)
66 Genetic variation in the Estonian population NC_000017.10 - 4371647 Oct 12, 2018 (152)
67 The Danish reference pan genome NC_000017.10 - 4371647 Apr 27, 2020 (154)
68 gnomAD - Genomes NC_000017.11 - 4468352 Apr 26, 2021 (155)
69 Genome of the Netherlands Release 5 NC_000017.10 - 4371647 Apr 27, 2020 (154)
70 KOREAN population from KRGDB NC_000017.10 - 4371647 Apr 27, 2020 (154)
71 Korean Genome Project NC_000017.11 - 4468352 Apr 27, 2020 (154)
72 Northern Sweden NC_000017.10 - 4371647 Jul 13, 2019 (153)
73 Qatari NC_000017.10 - 4371647 Apr 27, 2020 (154)
74 SGDP_PRJ NC_000017.10 - 4371647 Apr 27, 2020 (154)
75 Siberian NC_000017.10 - 4371647 Apr 27, 2020 (154)
76 8.3KJPN NC_000017.10 - 4371647 Apr 26, 2021 (155)
77 14KJPN NC_000017.11 - 4468352 Oct 16, 2022 (156)
78 TopMed NC_000017.11 - 4468352 Apr 26, 2021 (155)
79 UK 10K study - Twins NC_000017.10 - 4371647 Oct 12, 2018 (152)
80 A Vietnamese Genetic Variation Database NC_000017.10 - 4371647 Jul 13, 2019 (153)
81 ALFA NC_000017.11 - 4468352 Apr 26, 2021 (155)
Help

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
ss90515315, ss167693467, ss282672204, ss483631259, ss1696912667 NC_000017.9:4318395:A:C NC_000017.11:4468351:A:C (self)
70920847, 39333220, 27819388, 4273714, 17535636, 41996702, 15113742, 18360372, 37252550, 9909098, 79238380, 39333220, 8713948, ss227436971, ss237164066, ss243477764, ss482625919, ss534726050, ss565136101, ss660922914, ss780039130, ss781823780, ss835519616, ss992872192, ss1080896059, ss1357714064, ss1427961534, ss1578067816, ss1635188750, ss1678182783, ss1936318450, ss2028947166, ss2157392744, ss2633368466, ss2701934309, ss2947154639, ss3015113715, ss3351629035, ss3627612429, ss3631351386, ss3641980288, ss3682081140, ss3741828877, ss3754390541, ss3834752842, ss3840984678, ss3885235570, ss3934819308, ss5221269073, ss5315869277, ss5426081042, ss5659626430, ss5833652901, ss5951035437 NC_000017.10:4371646:A:C NC_000017.11:4468351:A:C (self)
93057581, 500107350, 34675189, 110632148, 243389341, 13535848917, ss2215121757, ss3028291970, ss3699986264, ss3819660023, ss3846478890, ss3978297188, ss5027843679, ss5302254033, ss5495447462, ss5605531646, ss5776795044, ss5816292473, ss5851717743, ss5913034831 NC_000017.11:4468351:A:C NC_000017.11:4468351:A:C (self)
ss136949046, ss157779366 NT_010718.16:3975020:A:C NC_000017.11:4468351:A:C (self)
Help

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

No publications for rs62064884

Help

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.

Software version is: 2.0.1.post761+d5e8e07