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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.

rs36078476

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr10:102066172 (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>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.009171 (2706/295066, ALFA)
G=0.006706 (1775/264690, TOPMED)
G=0.007485 (1873/250234, GnomAD_exome) (+ 13 more)
G=0.005918 (830/140258, GnomAD)
G=0.007479 (891/119130, ExAC)
G=0.00488 (384/78654, PAGE_STUDY)
G=0.00006 (1/16760, 8.3KJPN)
G=0.00684 (89/13006, GO-ESP)
G=0.0037 (24/6404, 1000G_30x)
G=0.0036 (18/5008, 1000G)
G=0.0016 (7/4480, Estonian)
G=0.0099 (38/3854, ALSPAC)
G=0.0081 (30/3708, TWINSUK)
G=0.006 (3/534, MGP)
G=0.015 (6/402, HapMap)
G=0.014 (3/216, Qatari)
Clinical Significance
Reported in ClinVar
Gene : Consequence
HPS6 : Missense Variant
Publications
1 citation
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 311544 T=0.990919 G=0.009081
European Sub 263842 T=0.990365 G=0.009635
African Sub 13454 T=0.99777 G=0.00223
African Others Sub 488 T=1.000 G=0.000
African American Sub 12966 T=0.99769 G=0.00231
Asian Sub 6860 T=1.0000 G=0.0000
East Asian Sub 4906 T=1.0000 G=0.0000
Other Asian Sub 1954 T=1.0000 G=0.0000
Latin American 1 Sub 1326 T=0.9917 G=0.0083
Latin American 2 Sub 2584 T=0.9946 G=0.0054
South Asian Sub 366 T=0.986 G=0.014
Other Sub 23112 T=0.99018 G=0.00982


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
Allele Frequency Aggregator Total Global 295066 T=0.990829 G=0.009171
Allele Frequency Aggregator European Sub 253654 T=0.990377 G=0.009623
Allele Frequency Aggregator Other Sub 21660 T=0.99026 G=0.00974
Allele Frequency Aggregator African Sub 8616 T=0.9972 G=0.0028
Allele Frequency Aggregator Asian Sub 6860 T=1.0000 G=0.0000
Allele Frequency Aggregator Latin American 2 Sub 2584 T=0.9946 G=0.0054
Allele Frequency Aggregator Latin American 1 Sub 1326 T=0.9917 G=0.0083
Allele Frequency Aggregator South Asian Sub 366 T=0.986 G=0.014
TopMed Global Study-wide 264690 T=0.993294 G=0.006706
gnomAD - Exomes Global Study-wide 250234 T=0.992515 G=0.007485
gnomAD - Exomes European Sub 134542 T=0.992917 G=0.007083
gnomAD - Exomes Asian Sub 48928 T=0.99227 G=0.00773
gnomAD - Exomes American Sub 34568 T=0.99540 G=0.00460
gnomAD - Exomes African Sub 16040 T=0.99825 G=0.00175
gnomAD - Exomes Ashkenazi Jewish Sub 10044 T=0.97013 G=0.02987
gnomAD - Exomes Other Sub 6112 T=0.9910 G=0.0090
gnomAD - Genomes Global Study-wide 140258 T=0.994082 G=0.005918
gnomAD - Genomes European Sub 75952 T=0.99297 G=0.00703
gnomAD - Genomes African Sub 42040 T=0.99838 G=0.00162
gnomAD - Genomes American Sub 13656 T=0.99063 G=0.00937
gnomAD - Genomes Ashkenazi Jewish Sub 3324 T=0.9741 G=0.0259
gnomAD - Genomes East Asian Sub 3132 T=0.9997 G=0.0003
gnomAD - Genomes Other Sub 2154 T=0.9940 G=0.0060
ExAC Global Study-wide 119130 T=0.992521 G=0.007479
ExAC Europe Sub 71682 T=0.99155 G=0.00845
ExAC Asian Sub 25086 T=0.99167 G=0.00833
ExAC American Sub 11530 T=0.99575 G=0.00425
ExAC African Sub 9946 T=0.9984 G=0.0016
ExAC Other Sub 886 T=0.988 G=0.012
The PAGE Study Global Study-wide 78654 T=0.99512 G=0.00488
The PAGE Study AfricanAmerican Sub 32472 T=0.99760 G=0.00240
The PAGE Study Mexican Sub 10810 T=0.99315 G=0.00685
The PAGE Study Asian Sub 8318 T=0.9998 G=0.0002
The PAGE Study PuertoRican Sub 7918 T=0.9855 G=0.0145
The PAGE Study NativeHawaiian Sub 4530 T=0.9993 G=0.0007
The PAGE Study Cuban Sub 4230 T=0.9913 G=0.0087
The PAGE Study Dominican Sub 3828 T=0.9919 G=0.0081
The PAGE Study CentralAmerican Sub 2450 T=0.9947 G=0.0053
The PAGE Study SouthAmerican Sub 1982 T=0.9960 G=0.0040
The PAGE Study NativeAmerican Sub 1260 T=0.9952 G=0.0048
The PAGE Study SouthAsian Sub 856 T=0.980 G=0.020
8.3KJPN JAPANESE Study-wide 16760 T=0.99994 G=0.00006
GO Exome Sequencing Project Global Study-wide 13006 T=0.99316 G=0.00684
GO Exome Sequencing Project European American Sub 8600 T=0.9902 G=0.0098
GO Exome Sequencing Project African American Sub 4406 T=0.9989 G=0.0011
1000Genomes_30x Global Study-wide 6404 T=0.9963 G=0.0037
1000Genomes_30x African Sub 1786 T=1.0000 G=0.0000
1000Genomes_30x Europe Sub 1266 T=0.9921 G=0.0079
1000Genomes_30x South Asian Sub 1202 T=0.9925 G=0.0075
1000Genomes_30x East Asian Sub 1170 T=1.0000 G=0.0000
1000Genomes_30x American Sub 980 T=0.995 G=0.005
1000Genomes Global Study-wide 5008 T=0.9964 G=0.0036
1000Genomes African Sub 1322 T=1.0000 G=0.0000
1000Genomes East Asian Sub 1008 T=1.0000 G=0.0000
1000Genomes Europe Sub 1006 T=0.9911 G=0.0089
1000Genomes South Asian Sub 978 T=0.995 G=0.005
1000Genomes American Sub 694 T=0.994 G=0.006
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.9984 G=0.0016
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.9901 G=0.0099
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.9919 G=0.0081
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 T=0.994 G=0.006
HapMap Global Study-wide 402 T=0.985 G=0.015
HapMap American Sub 226 T=0.991 G=0.009
HapMap Europe Sub 176 T=0.977 G=0.023
Qatari Global Study-wide 216 T=0.986 G=0.014
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 10 NC_000010.11:g.102066172T>G
GRCh37.p13 chr 10 NC_000010.10:g.103825929T>G
HPS6 RefSeqGene (LRG_564) NG_012029.1:g.5783T>G
Gene: HPS6, HPS6 biogenesis of lysosomal organelles complex 2 subunit 3 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
HPS6 transcript NM_024747.6:c.698T>G L [CTT] > R [CGT] Coding Sequence Variant
BLOC-2 complex member HPS6 NP_079023.2:p.Leu233Arg L (Leu) > R (Arg) Missense 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.

Allele: G (allele ID: 207733 )
ClinVar Accession Disease Names Clinical Significance
RCV000192381.10 not specified Benign-Likely-Benign
RCV000963272.7 not provided Benign
RCV001105417.3 Hermansky-Pudlak syndrome 6 Benign
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= G
GRCh38.p14 chr 10 NC_000010.11:g.102066172= NC_000010.11:g.102066172T>G
GRCh37.p13 chr 10 NC_000010.10:g.103825929= NC_000010.10:g.103825929T>G
HPS6 RefSeqGene (LRG_564) NG_012029.1:g.5783= NG_012029.1:g.5783T>G
HPS6 transcript NM_024747.6:c.698= NM_024747.6:c.698T>G
HPS6 transcript NM_024747.5:c.698= NM_024747.5:c.698T>G
BLOC-2 complex member HPS6 NP_079023.2:p.Leu233= NP_079023.2:p.Leu233Arg
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#.

91 SubSNP, 16 Frequency, 3 ClinVar submissions
No Submitter Submission ID Date (Build)
1 APPLERA_GI ss48413688 Mar 15, 2006 (126)
2 ILLUMINA ss74998530 Dec 06, 2007 (129)
3 KRIBB_YJKIM ss119920611 Dec 01, 2009 (131)
4 ILLUMINA ss160630339 Dec 01, 2009 (131)
5 ILLUMINA ss173608526 Jul 04, 2010 (132)
6 1000GENOMES ss336346761 May 09, 2011 (134)
7 NHLBI-ESP ss342306732 May 09, 2011 (134)
8 ILLUMINA ss480796997 May 04, 2012 (137)
9 ILLUMINA ss480812688 May 04, 2012 (137)
10 ILLUMINA ss481736240 Sep 08, 2015 (146)
11 ILLUMINA ss485193264 May 04, 2012 (137)
12 1000GENOMES ss491003641 May 04, 2012 (137)
13 EXOME_CHIP ss491439844 May 04, 2012 (137)
14 CLINSEQ_SNP ss491631520 May 04, 2012 (137)
15 ILLUMINA ss537182547 Sep 08, 2015 (146)
16 ILLUMINA ss779055410 Sep 08, 2015 (146)
17 ILLUMINA ss780890042 Sep 08, 2015 (146)
18 ILLUMINA ss783042690 Sep 08, 2015 (146)
19 ILLUMINA ss783576347 Sep 08, 2015 (146)
20 ILLUMINA ss784001860 Sep 08, 2015 (146)
21 ILLUMINA ss832300448 Sep 08, 2015 (146)
22 ILLUMINA ss834518448 Sep 08, 2015 (146)
23 EVA-GONL ss987856027 Aug 21, 2014 (142)
24 JMKIDD_LAB ss1067515781 Aug 21, 2014 (142)
25 JMKIDD_LAB ss1077250170 Aug 21, 2014 (142)
26 1000GENOMES ss1338818022 Aug 21, 2014 (142)
27 EVA_DECODE ss1597530649 Apr 01, 2015 (144)
28 EVA_UK10K_ALSPAC ss1625300874 Apr 01, 2015 (144)
29 EVA_UK10K_TWINSUK ss1668294907 Apr 01, 2015 (144)
30 EVA_EXAC ss1690052691 Apr 01, 2015 (144)
31 EVA_MGP ss1711268411 Apr 01, 2015 (144)
32 EVA_SVP ss1713206572 Apr 01, 2015 (144)
33 ILLUMINA ss1751943589 Sep 08, 2015 (146)
34 ILLUMINA ss1751943590 Sep 08, 2015 (146)
35 ILLUMINA ss1917850937 Feb 12, 2016 (147)
36 WEILL_CORNELL_DGM ss1931219973 Feb 12, 2016 (147)
37 ILLUMINA ss1946291711 Feb 12, 2016 (147)
38 ILLUMINA ss1959289820 Feb 12, 2016 (147)
39 HUMAN_LONGEVITY ss2177555092 Dec 20, 2016 (150)
40 ILLUMINA ss2632754830 Nov 08, 2017 (151)
41 GNOMAD ss2738484337 Nov 08, 2017 (151)
42 GNOMAD ss2748459967 Nov 08, 2017 (151)
43 GNOMAD ss2892695492 Nov 08, 2017 (151)
44 AFFY ss2984921985 Nov 08, 2017 (151)
45 SWEGEN ss3007048219 Nov 08, 2017 (151)
46 ILLUMINA ss3021269911 Nov 08, 2017 (151)
47 CSHL ss3349283078 Nov 08, 2017 (151)
48 ILLUMINA ss3625585995 Oct 12, 2018 (152)
49 ILLUMINA ss3626521447 Oct 12, 2018 (152)
50 ILLUMINA ss3626521448 Oct 12, 2018 (152)
51 ILLUMINA ss3630777578 Oct 12, 2018 (152)
52 ILLUMINA ss3633660087 Oct 12, 2018 (152)
53 ILLUMINA ss3634421044 Oct 12, 2018 (152)
54 ILLUMINA ss3634421045 Oct 12, 2018 (152)
55 ILLUMINA ss3635352300 Oct 12, 2018 (152)
56 ILLUMINA ss3636105570 Oct 12, 2018 (152)
57 ILLUMINA ss3637103026 Oct 12, 2018 (152)
58 ILLUMINA ss3637870621 Oct 12, 2018 (152)
59 ILLUMINA ss3640128385 Oct 12, 2018 (152)
60 ILLUMINA ss3640128386 Oct 12, 2018 (152)
61 ILLUMINA ss3642872366 Oct 12, 2018 (152)
62 ILLUMINA ss3644544460 Oct 12, 2018 (152)
63 OMUKHERJEE_ADBS ss3646414764 Oct 12, 2018 (152)
64 ILLUMINA ss3651628842 Oct 12, 2018 (152)
65 ILLUMINA ss3653692836 Oct 12, 2018 (152)
66 EGCUT_WGS ss3674459535 Jul 13, 2019 (153)
67 ILLUMINA ss3725184034 Jul 13, 2019 (153)
68 ILLUMINA ss3744371116 Jul 13, 2019 (153)
69 ILLUMINA ss3744721993 Jul 13, 2019 (153)
70 ILLUMINA ss3744721994 Jul 13, 2019 (153)
71 PAGE_CC ss3771579489 Jul 13, 2019 (153)
72 ILLUMINA ss3772222318 Jul 13, 2019 (153)
73 ILLUMINA ss3772222319 Jul 13, 2019 (153)
74 EVA ss3824549658 Apr 26, 2020 (154)
75 EVA ss3825782764 Apr 26, 2020 (154)
76 FSA-LAB ss3983985350 Apr 27, 2021 (155)
77 EVA ss3986496827 Apr 27, 2021 (155)
78 EVA ss4017504519 Apr 27, 2021 (155)
79 TOPMED ss4864352609 Apr 27, 2021 (155)
80 TOMMO_GENOMICS ss5199199086 Apr 27, 2021 (155)
81 1000G_HIGH_COVERAGE ss5285257832 Oct 16, 2022 (156)
82 EVA ss5395635658 Oct 16, 2022 (156)
83 HUGCELL_USP ss5480700143 Oct 16, 2022 (156)
84 1000G_HIGH_COVERAGE ss5579820478 Oct 16, 2022 (156)
85 SANFORD_IMAGENETICS ss5649978823 Oct 16, 2022 (156)
86 EVA ss5824875189 Oct 16, 2022 (156)
87 EVA ss5847608024 Oct 16, 2022 (156)
88 EVA ss5848306657 Oct 16, 2022 (156)
89 EVA ss5880281257 Oct 16, 2022 (156)
90 EVA ss5941270440 Oct 16, 2022 (156)
91 EVA ss5979337152 Oct 16, 2022 (156)
92 1000Genomes NC_000010.10 - 103825929 Oct 12, 2018 (152)
93 1000Genomes_30x NC_000010.11 - 102066172 Oct 16, 2022 (156)
94 The Avon Longitudinal Study of Parents and Children NC_000010.10 - 103825929 Oct 12, 2018 (152)
95 Genetic variation in the Estonian population NC_000010.10 - 103825929 Oct 12, 2018 (152)
96 ExAC NC_000010.10 - 103825929 Oct 12, 2018 (152)
97 gnomAD - Genomes NC_000010.11 - 102066172 Apr 27, 2021 (155)
98 gnomAD - Exomes NC_000010.10 - 103825929 Jul 13, 2019 (153)
99 GO Exome Sequencing Project NC_000010.10 - 103825929 Oct 12, 2018 (152)
100 HapMap NC_000010.11 - 102066172 Apr 26, 2020 (154)
101 Medical Genome Project healthy controls from Spanish population NC_000010.10 - 103825929 Apr 26, 2020 (154)
102 The PAGE Study NC_000010.11 - 102066172 Jul 13, 2019 (153)
103 Qatari NC_000010.10 - 103825929 Apr 26, 2020 (154)
104 8.3KJPN NC_000010.10 - 103825929 Apr 27, 2021 (155)
105 TopMed NC_000010.11 - 102066172 Apr 27, 2021 (155)
106 UK 10K study - Twins NC_000010.10 - 103825929 Oct 12, 2018 (152)
107 ALFA NC_000010.11 - 102066172 Apr 27, 2021 (155)
108 ClinVar RCV000192381.10 Oct 16, 2022 (156)
109 ClinVar RCV000963272.7 Oct 16, 2022 (156)
110 ClinVar RCV001105417.3 Oct 16, 2022 (156)
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)
rs386584412 Aug 21, 2014 (142)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss480796997, ss491631520, ss1597530649, ss1713206572, ss3642872366 NC_000010.9:103815918:T:G NC_000010.11:102066171:T:G (self)
51256474, 28461397, 20197783, 285103, 7685937, 1007331, 384171, 13261903, 57168393, 28461397, ss336346761, ss342306732, ss480812688, ss481736240, ss485193264, ss491003641, ss491439844, ss537182547, ss779055410, ss780890042, ss783042690, ss783576347, ss784001860, ss832300448, ss834518448, ss987856027, ss1067515781, ss1077250170, ss1338818022, ss1625300874, ss1668294907, ss1690052691, ss1711268411, ss1751943589, ss1751943590, ss1917850937, ss1931219973, ss1946291711, ss1959289820, ss2632754830, ss2738484337, ss2748459967, ss2892695492, ss2984921985, ss3007048219, ss3021269911, ss3349283078, ss3625585995, ss3626521447, ss3626521448, ss3630777578, ss3633660087, ss3634421044, ss3634421045, ss3635352300, ss3636105570, ss3637103026, ss3637870621, ss3640128385, ss3640128386, ss3644544460, ss3646414764, ss3651628842, ss3653692836, ss3674459535, ss3744371116, ss3744721993, ss3744721994, ss3772222318, ss3772222319, ss3824549658, ss3825782764, ss3983985350, ss3986496827, ss4017504519, ss5199199086, ss5395635658, ss5649978823, ss5824875189, ss5847608024, ss5848306657, ss5941270440, ss5979337152 NC_000010.10:103825928:T:G NC_000010.11:102066171:T:G (self)
RCV000192381.10, RCV000963272.7, RCV001105417.3, 67346413, 362191419, 477897, 800958, 79898264, 5545223365, ss2177555092, ss3725184034, ss3771579489, ss4864352609, ss5285257832, ss5480700143, ss5579820478, ss5880281257 NC_000010.11:102066171:T:G NC_000010.11:102066171:T:G (self)
ss48413688, ss74998530, ss119920611, ss160630339, ss173608526 NT_030059.13:54630392:T:G NC_000010.11:102066171: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.

1 citation for rs36078476
PMID Title Author Year Journal
25741868 Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Richards S et al. 2015 Genetics in medicine
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