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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.

rs6416879

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr17:4467775 (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
T>A / T>C / T>G
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.122528 (32432/264690, TOPMED)
T=0.133494 (18711/140164, GnomAD)
T=0.00018 (5/28258, 14KJPN) (+ 16 more)
T=0.15733 (2972/18890, ALFA)
T=0.00024 (4/16760, 8.3KJPN)
T=0.0757 (485/6404, 1000G_30x)
T=0.0773 (387/5008, 1000G)
T=0.1656 (742/4480, Estonian)
T=0.1842 (710/3854, ALSPAC)
T=0.1799 (667/3708, TWINSUK)
T=0.0007 (2/2930, KOREAN)
T=0.0005 (1/1832, Korea1K)
T=0.190 (190/998, GoNL)
T=0.185 (111/600, NorthernSweden)
T=0.078 (43/550, SGDP_PRJ)
T=0.245 (53/216, Qatari)
T=0.005 (1/212, Vietnamese)
T=0.06 (3/54, Siberian)
T=0.17 (7/40, GENOME_DK)
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 18890 T=0.15733 C=0.84267
European Sub 14286 T=0.18410 C=0.81590
African Sub 2946 T=0.0526 C=0.9474
African Others Sub 114 T=0.053 C=0.947
African American Sub 2832 T=0.0526 C=0.9474
Asian Sub 112 T=0.000 C=1.000
East Asian Sub 86 T=0.00 C=1.00
Other Asian Sub 26 T=0.00 C=1.00
Latin American 1 Sub 146 T=0.137 C=0.863
Latin American 2 Sub 610 T=0.093 C=0.907
South Asian Sub 98 T=0.09 C=0.91
Other Sub 692 T=0.146 C=0.854


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 T=0.122528 C=0.877472
gnomAD - Genomes Global Study-wide 140164 T=0.133494 C=0.866506
gnomAD - Genomes European Sub 75894 T=0.18535 C=0.81465
gnomAD - Genomes African Sub 42012 T=0.05118 C=0.94882
gnomAD - Genomes American Sub 13652 T=0.11332 C=0.88668
gnomAD - Genomes Ashkenazi Jewish Sub 3320 T=0.1910 C=0.8090
gnomAD - Genomes East Asian Sub 3134 T=0.0006 C=0.9994
gnomAD - Genomes Other Sub 2152 T=0.1445 C=0.8555
14KJPN JAPANESE Study-wide 28258 T=0.00018 C=0.99982
Allele Frequency Aggregator Total Global 18890 T=0.15733 C=0.84267
Allele Frequency Aggregator European Sub 14286 T=0.18410 C=0.81590
Allele Frequency Aggregator African Sub 2946 T=0.0526 C=0.9474
Allele Frequency Aggregator Other Sub 692 T=0.146 C=0.854
Allele Frequency Aggregator Latin American 2 Sub 610 T=0.093 C=0.907
Allele Frequency Aggregator Latin American 1 Sub 146 T=0.137 C=0.863
Allele Frequency Aggregator Asian Sub 112 T=0.000 C=1.000
Allele Frequency Aggregator South Asian Sub 98 T=0.09 C=0.91
8.3KJPN JAPANESE Study-wide 16760 T=0.00024 C=0.99976
1000Genomes_30x Global Study-wide 6404 T=0.0757 C=0.9243
1000Genomes_30x African Sub 1786 T=0.0347 C=0.9653
1000Genomes_30x Europe Sub 1266 T=0.1912 C=0.8088
1000Genomes_30x South Asian Sub 1202 T=0.0707 C=0.9293
1000Genomes_30x East Asian Sub 1170 T=0.0000 C=1.0000
1000Genomes_30x American Sub 980 T=0.098 C=0.902
1000Genomes Global Study-wide 5008 T=0.0773 C=0.9227
1000Genomes African Sub 1322 T=0.0340 C=0.9660
1000Genomes East Asian Sub 1008 T=0.0000 C=1.0000
1000Genomes Europe Sub 1006 T=0.1998 C=0.8002
1000Genomes South Asian Sub 978 T=0.072 C=0.928
1000Genomes American Sub 694 T=0.102 C=0.898
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.1656 C=0.8344
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.1842 C=0.8158
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.1799 C=0.8201
KOREAN population from KRGDB KOREAN Study-wide 2930 T=0.0007 A=0.0000, C=0.9993, G=0.0000
Korean Genome Project KOREAN Study-wide 1832 T=0.0005 C=0.9995
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 T=0.190 C=0.810
Northern Sweden ACPOP Study-wide 600 T=0.185 C=0.815
SGDP_PRJ Global Study-wide 550 T=0.078 C=0.922
Qatari Global Study-wide 216 T=0.245 C=0.755
A Vietnamese Genetic Variation Database Global Study-wide 212 T=0.005 C=0.995
Siberian Global Study-wide 54 T=0.06 C=0.94
The Danish reference pan genome Danish Study-wide 40 T=0.17 C=0.82
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.4467775T>A
GRCh38.p14 chr 17 NC_000017.11:g.4467775T>C
GRCh38.p14 chr 17 NC_000017.11:g.4467775T>G
GRCh37.p13 chr 17 NC_000017.10:g.4371070T>A
GRCh37.p13 chr 17 NC_000017.10:g.4371070T>C
GRCh37.p13 chr 17 NC_000017.10:g.4371070T>G
Gene: SPNS3, sphingolipid transporter 3 (putative) (plus strand)
Molecule type Change Amino acid[Codon] SO Term
SPNS3 transcript variant 2 NM_001320449.2:c.733-1079…

NM_001320449.2:c.733-10797T>A

N/A Intron Variant
SPNS3 transcript variant 1 NM_182538.5:c.1114-10797T…

NM_182538.5:c.1114-10797T>A

N/A Intron Variant
SPNS3 transcript variant X1 XM_011523723.1:c.1113+145…

XM_011523723.1:c.1113+14570T>A

N/A Intron Variant
SPNS3 transcript variant X2 XM_011523724.1:c.1114-107…

XM_011523724.1:c.1114-10797T>A

N/A Intron Variant
SPNS3 transcript variant X3 XM_011523725.1:c.961-1079…

XM_011523725.1:c.961-10797T>A

N/A Intron Variant
SPNS3 transcript variant X7 XM_011523728.3:c.526-1079…

XM_011523728.3:c.526-10797T>A

N/A Intron Variant
SPNS3 transcript variant X8 XM_017024345.3:c.388-1079…

XM_017024345.3:c.388-10797T>A

N/A Intron Variant
SPNS3 transcript variant X5 XM_047435588.1:c.775-1079…

XM_047435588.1:c.775-10797T>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
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 T= A C G
GRCh38.p14 chr 17 NC_000017.11:g.4467775= NC_000017.11:g.4467775T>A NC_000017.11:g.4467775T>C NC_000017.11:g.4467775T>G
GRCh37.p13 chr 17 NC_000017.10:g.4371070= NC_000017.10:g.4371070T>A NC_000017.10:g.4371070T>C NC_000017.10:g.4371070T>G
SPNS3 transcript variant 2 NM_001320449.2:c.733-10797= NM_001320449.2:c.733-10797T>A NM_001320449.2:c.733-10797T>C NM_001320449.2:c.733-10797T>G
SPNS3 transcript variant 1 NM_182538.4:c.1114-10797= NM_182538.4:c.1114-10797T>A NM_182538.4:c.1114-10797T>C NM_182538.4:c.1114-10797T>G
SPNS3 transcript variant 1 NM_182538.5:c.1114-10797= NM_182538.5:c.1114-10797T>A NM_182538.5:c.1114-10797T>C NM_182538.5:c.1114-10797T>G
SPNS3 transcript variant X1 XM_005256520.1:c.733-10797= XM_005256520.1:c.733-10797T>A XM_005256520.1:c.733-10797T>C XM_005256520.1:c.733-10797T>G
SPNS3 transcript variant X1 XM_011523723.1:c.1113+14570= XM_011523723.1:c.1113+14570T>A XM_011523723.1:c.1113+14570T>C XM_011523723.1:c.1113+14570T>G
SPNS3 transcript variant X2 XM_011523724.1:c.1114-10797= XM_011523724.1:c.1114-10797T>A XM_011523724.1:c.1114-10797T>C XM_011523724.1:c.1114-10797T>G
SPNS3 transcript variant X3 XM_011523725.1:c.961-10797= XM_011523725.1:c.961-10797T>A XM_011523725.1:c.961-10797T>C XM_011523725.1:c.961-10797T>G
SPNS3 transcript variant X7 XM_011523728.3:c.526-10797= XM_011523728.3:c.526-10797T>A XM_011523728.3:c.526-10797T>C XM_011523728.3:c.526-10797T>G
SPNS3 transcript variant X8 XM_017024345.3:c.388-10797= XM_017024345.3:c.388-10797T>A XM_017024345.3:c.388-10797T>C XM_017024345.3:c.388-10797T>G
SPNS3 transcript variant X5 XM_047435588.1:c.775-10797= XM_047435588.1:c.775-10797T>A XM_047435588.1:c.775-10797T>C XM_047435588.1:c.775-10797T>G
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#.

69 SubSNP, 19 Frequency submissions
No Submitter Submission ID Date (Build)
1 BCM_SSAHASNP ss10877213 Jul 11, 2003 (116)
2 SC_JCM ss11329145 Jul 11, 2003 (116)
3 WI_SSAHASNP ss12412783 Jul 11, 2003 (116)
4 BCM_SSAHASNP ss14283260 Dec 05, 2003 (119)
5 ABI ss40816928 Mar 15, 2006 (126)
6 HGSV ss77233643 Dec 07, 2007 (129)
7 HGSV ss84664590 Dec 15, 2007 (130)
8 BCMHGSC_JDW ss90515308 Mar 24, 2008 (129)
9 HUMANGENOME_JCVI ss96576028 Feb 06, 2009 (130)
10 ENSEMBL ss136949037 Dec 01, 2009 (131)
11 ENSEMBL ss143212307 Dec 01, 2009 (131)
12 GMI ss157779339 Dec 01, 2009 (131)
13 COMPLETE_GENOMICS ss167693427 Jul 04, 2010 (132)
14 BUSHMAN ss202150711 Jul 04, 2010 (132)
15 BL ss255451364 May 09, 2011 (134)
16 GMI ss282672200 May 04, 2012 (137)
17 GMI ss287138121 Apr 25, 2013 (138)
18 PJP ss291962329 May 09, 2011 (134)
19 1000GENOMES ss339523212 May 09, 2011 (134)
20 TISHKOFF ss565136093 Apr 25, 2013 (138)
21 SSMP ss660922909 Apr 25, 2013 (138)
22 EVA-GONL ss992872184 Aug 21, 2014 (142)
23 JMKIDD_LAB ss1080896049 Aug 21, 2014 (142)
24 1000GENOMES ss1357714042 Aug 21, 2014 (142)
25 DDI ss1427961530 Apr 01, 2015 (144)
26 EVA_GENOME_DK ss1578067811 Apr 01, 2015 (144)
27 EVA_UK10K_ALSPAC ss1635188737 Apr 01, 2015 (144)
28 EVA_UK10K_TWINSUK ss1678182770 Apr 01, 2015 (144)
29 EVA_DECODE ss1696912657 Apr 01, 2015 (144)
30 HAMMER_LAB ss1808680391 Sep 08, 2015 (146)
31 WEILL_CORNELL_DGM ss1936318438 Feb 12, 2016 (147)
32 GENOMED ss1968341091 Jul 19, 2016 (147)
33 JJLAB ss2028947159 Sep 14, 2016 (149)
34 USC_VALOUEV ss2157392738 Dec 20, 2016 (150)
35 HUMAN_LONGEVITY ss2215121712 Dec 20, 2016 (150)
36 SYSTEMSBIOZJU ss2628964484 Nov 08, 2017 (151)
37 GRF ss2701934305 Nov 08, 2017 (151)
38 GNOMAD ss2947154578 Nov 08, 2017 (151)
39 SWEGEN ss3015113706 Nov 08, 2017 (151)
40 BIOINF_KMB_FNS_UNIBA ss3028291966 Nov 08, 2017 (151)
41 CSHL ss3351629031 Nov 08, 2017 (151)
42 URBANLAB ss3650592291 Oct 12, 2018 (152)
43 EGCUT_WGS ss3682081130 Jul 13, 2019 (153)
44 EVA_DECODE ss3699986250 Jul 13, 2019 (153)
45 ACPOP ss3741828870 Jul 13, 2019 (153)
46 EVA ss3754390536 Jul 13, 2019 (153)
47 PACBIO ss3788135597 Jul 13, 2019 (153)
48 PACBIO ss3793105927 Jul 13, 2019 (153)
49 PACBIO ss3797991498 Jul 13, 2019 (153)
50 KHV_HUMAN_GENOMES ss3819660013 Jul 13, 2019 (153)
51 EVA ss3834752837 Apr 27, 2020 (154)
52 EVA ss3840984673 Apr 27, 2020 (154)
53 EVA ss3846478885 Apr 27, 2020 (154)
54 SGDP_PRJ ss3885235554 Apr 27, 2020 (154)
55 KRGDB ss3934819300 Apr 27, 2020 (154)
56 KOGIC ss3978297178 Apr 27, 2020 (154)
57 TOPMED ss5027843498 Apr 26, 2021 (155)
58 TOMMO_GENOMICS ss5221269057 Apr 26, 2021 (155)
59 1000G_HIGH_COVERAGE ss5302254009 Oct 16, 2022 (156)
60 HUGCELL_USP ss5495447440 Oct 16, 2022 (156)
61 1000G_HIGH_COVERAGE ss5605531614 Oct 16, 2022 (156)
62 SANFORD_IMAGENETICS ss5659626413 Oct 16, 2022 (156)
63 TOMMO_GENOMICS ss5776795025 Oct 16, 2022 (156)
64 YY_MCH ss5816292469 Oct 16, 2022 (156)
65 EVA ss5833652890 Oct 16, 2022 (156)
66 EVA ss5851717739 Oct 16, 2022 (156)
67 EVA ss5913034806 Oct 16, 2022 (156)
68 EVA ss5951035424 Oct 16, 2022 (156)
69 EVA ss5980947503 Oct 16, 2022 (156)
70 1000Genomes NC_000017.10 - 4371070 Oct 12, 2018 (152)
71 1000Genomes_30x NC_000017.11 - 4467775 Oct 16, 2022 (156)
72 The Avon Longitudinal Study of Parents and Children NC_000017.10 - 4371070 Oct 12, 2018 (152)
73 Genetic variation in the Estonian population NC_000017.10 - 4371070 Oct 12, 2018 (152)
74 The Danish reference pan genome NC_000017.10 - 4371070 Apr 27, 2020 (154)
75 gnomAD - Genomes NC_000017.11 - 4467775 Apr 26, 2021 (155)
76 Genome of the Netherlands Release 5 NC_000017.10 - 4371070 Apr 27, 2020 (154)
77 KOREAN population from KRGDB NC_000017.10 - 4371070 Apr 27, 2020 (154)
78 Korean Genome Project NC_000017.11 - 4467775 Apr 27, 2020 (154)
79 Northern Sweden NC_000017.10 - 4371070 Jul 13, 2019 (153)
80 Qatari NC_000017.10 - 4371070 Apr 27, 2020 (154)
81 SGDP_PRJ NC_000017.10 - 4371070 Apr 27, 2020 (154)
82 Siberian NC_000017.10 - 4371070 Apr 27, 2020 (154)
83 8.3KJPN NC_000017.10 - 4371070 Apr 26, 2021 (155)
84 14KJPN NC_000017.11 - 4467775 Oct 16, 2022 (156)
85 TopMed NC_000017.11 - 4467775 Apr 26, 2021 (155)
86 UK 10K study - Twins NC_000017.10 - 4371070 Oct 12, 2018 (152)
87 A Vietnamese Genetic Variation Database NC_000017.10 - 4371070 Jul 13, 2019 (153)
88 ALFA NC_000017.11 - 4467775 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).

Associated ID History Updated (Build)
rs60391836 May 25, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
41996694, ss3934819300 NC_000017.10:4371069:T:A NC_000017.11:4467774:T:A (self)
ss77233643, ss84664590, ss90515308, ss167693427, ss202150711, ss255451364, ss282672200, ss287138121, ss291962329, ss1696912657 NC_000017.9:4317818:T:C NC_000017.11:4467774:T:C (self)
70920824, 39333206, 27819378, 4273709, 17535628, 41996694, 15113735, 18360360, 37252534, 9909092, 79238364, 39333206, 8713942, ss339523212, ss565136093, ss660922909, ss992872184, ss1080896049, ss1357714042, ss1427961530, ss1578067811, ss1635188737, ss1678182770, ss1808680391, ss1936318438, ss1968341091, ss2028947159, ss2157392738, ss2628964484, ss2701934305, ss2947154578, ss3015113706, ss3351629031, ss3682081130, ss3741828870, ss3754390536, ss3788135597, ss3793105927, ss3797991498, ss3834752837, ss3840984673, ss3885235554, ss3934819300, ss5221269057, ss5659626413, ss5833652890, ss5951035424, ss5980947503 NC_000017.10:4371069:T:C NC_000017.11:4467774:T:C (self)
93057549, 500107213, 34675179, 110632129, 243389160, 7078174414, ss2215121712, ss3028291966, ss3650592291, ss3699986250, ss3819660013, ss3846478885, ss3978297178, ss5027843498, ss5302254009, ss5495447440, ss5605531614, ss5776795025, ss5816292469, ss5851717739, ss5913034806 NC_000017.11:4467774:T:C NC_000017.11:4467774:T:C (self)
ss10877213, ss11329145, ss12412783 NT_010718.13:3217959:T:C NC_000017.11:4467774:T:C (self)
ss14283260 NT_010718.14:3218099:T:C NC_000017.11:4467774:T:C (self)
ss40816928, ss96576028, ss136949037, ss143212307, ss157779339 NT_010718.16:3974443:T:C NC_000017.11:4467774:T:C (self)
41996694, ss3934819300 NC_000017.10:4371069:T:G NC_000017.11:4467774:T:G (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 rs6416879

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