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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.

rs6473891

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr8:53779049 (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 / A>G / A>T
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.110752 (29315/264690, TOPMED)
A=0.119057 (16689/140176, GnomAD)
A=0.09162 (2589/28258, 14KJPN) (+ 17 more)
A=0.13968 (2477/17734, ALFA)
A=0.08926 (1496/16760, 8.3KJPN)
A=0.1038 (665/6404, 1000G_30x)
A=0.1072 (537/5008, 1000G)
A=0.1560 (699/4480, Estonian)
A=0.1707 (658/3854, ALSPAC)
A=0.1669 (619/3708, TWINSUK)
A=0.0724 (212/2930, KOREAN)
A=0.0710 (130/1832, Korea1K)
A=0.155 (155/998, GoNL)
A=0.182 (109/600, NorthernSweden)
A=0.111 (60/542, SGDP_PRJ)
A=0.079 (26/328, HapMap)
A=0.222 (48/216, Qatari)
A=0.162 (35/216, Vietnamese)
A=0.13 (7/54, Siberian)
A=0.15 (6/40, GENOME_DK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
ATP6V1H : 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 17734 A=0.13968 G=0.86032, T=0.00000
European Sub 13656 A=0.16132 G=0.83868, T=0.00000
African Sub 2424 A=0.0309 G=0.9691, T=0.0000
African Others Sub 90 A=0.01 G=0.99, T=0.00
African American Sub 2334 A=0.0317 G=0.9683, T=0.0000
Asian Sub 112 A=0.134 G=0.866, T=0.000
East Asian Sub 86 A=0.14 G=0.86, T=0.00
Other Asian Sub 26 A=0.12 G=0.88, T=0.00
Latin American 1 Sub 146 A=0.082 G=0.918, T=0.000
Latin American 2 Sub 610 A=0.097 G=0.903, T=0.000
South Asian Sub 98 A=0.27 G=0.73, T=0.00
Other Sub 688 A=0.126 G=0.874, T=0.000


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=0.110752 G=0.889248
gnomAD - Genomes Global Study-wide 140176 A=0.119057 G=0.880943
gnomAD - Genomes European Sub 75896 A=0.16715 G=0.83285
gnomAD - Genomes African Sub 42028 A=0.03126 G=0.96874
gnomAD - Genomes American Sub 13644 A=0.10657 G=0.89343
gnomAD - Genomes Ashkenazi Jewish Sub 3324 A=0.1883 G=0.8117
gnomAD - Genomes East Asian Sub 3132 A=0.1191 G=0.8809
gnomAD - Genomes Other Sub 2152 A=0.1097 G=0.8903
14KJPN JAPANESE Study-wide 28258 A=0.09162 G=0.90838
Allele Frequency Aggregator Total Global 17734 A=0.13968 G=0.86032, T=0.00000
Allele Frequency Aggregator European Sub 13656 A=0.16132 G=0.83868, T=0.00000
Allele Frequency Aggregator African Sub 2424 A=0.0309 G=0.9691, T=0.0000
Allele Frequency Aggregator Other Sub 688 A=0.126 G=0.874, T=0.000
Allele Frequency Aggregator Latin American 2 Sub 610 A=0.097 G=0.903, T=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 A=0.082 G=0.918, T=0.000
Allele Frequency Aggregator Asian Sub 112 A=0.134 G=0.866, T=0.000
Allele Frequency Aggregator South Asian Sub 98 A=0.27 G=0.73, T=0.00
8.3KJPN JAPANESE Study-wide 16760 A=0.08926 G=0.91074
1000Genomes_30x Global Study-wide 6404 A=0.1038 G=0.8962
1000Genomes_30x African Sub 1786 A=0.0084 G=0.9916
1000Genomes_30x Europe Sub 1266 A=0.1556 G=0.8444
1000Genomes_30x South Asian Sub 1202 A=0.1772 G=0.8228
1000Genomes_30x East Asian Sub 1170 A=0.1222 G=0.8778
1000Genomes_30x American Sub 980 A=0.099 G=0.901
1000Genomes Global Study-wide 5008 A=0.1072 G=0.8928
1000Genomes African Sub 1322 A=0.0091 G=0.9909
1000Genomes East Asian Sub 1008 A=0.1230 G=0.8770
1000Genomes Europe Sub 1006 A=0.1581 G=0.8419
1000Genomes South Asian Sub 978 A=0.175 G=0.825
1000Genomes American Sub 694 A=0.102 G=0.898
Genetic variation in the Estonian population Estonian Study-wide 4480 A=0.1560 G=0.8440
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.1707 G=0.8293
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.1669 G=0.8331
KOREAN population from KRGDB KOREAN Study-wide 2930 A=0.0724 C=0.0000, G=0.9276, T=0.0000
Korean Genome Project KOREAN Study-wide 1832 A=0.0710 G=0.9290
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 A=0.155 G=0.845
Northern Sweden ACPOP Study-wide 600 A=0.182 G=0.818
SGDP_PRJ Global Study-wide 542 A=0.111 G=0.889
HapMap Global Study-wide 328 A=0.079 G=0.921
HapMap African Sub 120 A=0.000 G=1.000
HapMap American Sub 120 A=0.133 G=0.867
HapMap Asian Sub 88 A=0.11 G=0.89
Qatari Global Study-wide 216 A=0.222 G=0.778
A Vietnamese Genetic Variation Database Global Study-wide 216 A=0.162 G=0.838
Siberian Global Study-wide 54 A=0.13 G=0.87
The Danish reference pan genome Danish Study-wide 40 A=0.15 G=0.85
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 8 NC_000008.11:g.53779049A>C
GRCh38.p14 chr 8 NC_000008.11:g.53779049A>G
GRCh38.p14 chr 8 NC_000008.11:g.53779049A>T
GRCh37.p13 chr 8 NC_000008.10:g.54691609A>C
GRCh37.p13 chr 8 NC_000008.10:g.54691609A>G
GRCh37.p13 chr 8 NC_000008.10:g.54691609A>T
Gene: ATP6V1H, ATPase H+ transporting V1 subunit H (minus strand)
Molecule type Change Amino acid[Codon] SO Term
ATP6V1H transcript variant 1 NM_015941.4:c.871-6882T>G N/A Intron Variant
ATP6V1H transcript variant 2 NM_213619.3:c.817-6882T>G N/A Intron Variant
ATP6V1H transcript variant 3 NM_213620.3:c.871-6882T>G N/A Intron Variant
ATP6V1H transcript variant X1 XM_006716455.4:c.817-6882…

XM_006716455.4:c.817-6882T>G

N/A Intron Variant
ATP6V1H transcript variant X2 XM_011517542.2:c.250-6882…

XM_011517542.2:c.250-6882T>G

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 G T
GRCh38.p14 chr 8 NC_000008.11:g.53779049= NC_000008.11:g.53779049A>C NC_000008.11:g.53779049A>G NC_000008.11:g.53779049A>T
GRCh37.p13 chr 8 NC_000008.10:g.54691609= NC_000008.10:g.54691609A>C NC_000008.10:g.54691609A>G NC_000008.10:g.54691609A>T
ATP6V1H transcript variant 1 NM_015941.3:c.871-6882= NM_015941.3:c.871-6882T>G NM_015941.3:c.871-6882T>C NM_015941.3:c.871-6882T>A
ATP6V1H transcript variant 1 NM_015941.4:c.871-6882= NM_015941.4:c.871-6882T>G NM_015941.4:c.871-6882T>C NM_015941.4:c.871-6882T>A
ATP6V1H transcript variant 2 NM_213619.2:c.817-6882= NM_213619.2:c.817-6882T>G NM_213619.2:c.817-6882T>C NM_213619.2:c.817-6882T>A
ATP6V1H transcript variant 2 NM_213619.3:c.817-6882= NM_213619.3:c.817-6882T>G NM_213619.3:c.817-6882T>C NM_213619.3:c.817-6882T>A
ATP6V1H transcript variant 3 NM_213620.2:c.871-6882= NM_213620.2:c.871-6882T>G NM_213620.2:c.871-6882T>C NM_213620.2:c.871-6882T>A
ATP6V1H transcript variant 3 NM_213620.3:c.871-6882= NM_213620.3:c.871-6882T>G NM_213620.3:c.871-6882T>C NM_213620.3:c.871-6882T>A
ATP6V1H transcript variant X1 XM_005251257.1:c.871-6882= XM_005251257.1:c.871-6882T>G XM_005251257.1:c.871-6882T>C XM_005251257.1:c.871-6882T>A
ATP6V1H transcript variant X2 XM_005251258.1:c.793-6882= XM_005251258.1:c.793-6882T>G XM_005251258.1:c.793-6882T>C XM_005251258.1:c.793-6882T>A
ATP6V1H transcript variant X3 XM_005251259.1:c.751-6882= XM_005251259.1:c.751-6882T>G XM_005251259.1:c.751-6882T>C XM_005251259.1:c.751-6882T>A
ATP6V1H transcript variant X1 XM_006716455.4:c.817-6882= XM_006716455.4:c.817-6882T>G XM_006716455.4:c.817-6882T>C XM_006716455.4:c.817-6882T>A
ATP6V1H transcript variant X2 XM_011517542.2:c.250-6882= XM_011517542.2:c.250-6882T>G XM_011517542.2:c.250-6882T>C XM_011517542.2:c.250-6882T>A
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#.

79 SubSNP, 20 Frequency submissions
No Submitter Submission ID Date (Build)
1 BCM_SSAHASNP ss10484563 Jul 11, 2003 (116)
2 WI_SSAHASNP ss11967479 Jul 11, 2003 (116)
3 WI_SSAHASNP ss14337538 Dec 05, 2003 (119)
4 WUGSC_SSAHASNP ss14526133 Dec 05, 2003 (119)
5 CSHL-HAPMAP ss17232397 Feb 27, 2004 (120)
6 ABI ss44856924 Mar 13, 2006 (126)
7 HGSV ss77270369 Dec 07, 2007 (129)
8 HGSV ss78156064 Dec 07, 2007 (129)
9 HGSV ss78748943 Dec 07, 2007 (129)
10 BCMHGSC_JDW ss93888205 Mar 25, 2008 (129)
11 HUMANGENOME_JCVI ss97873704 Feb 04, 2009 (130)
12 BGI ss105618722 Feb 04, 2009 (130)
13 1000GENOMES ss108030518 Jan 22, 2009 (130)
14 1000GENOMES ss115405416 Jan 25, 2009 (130)
15 ILLUMINA-UK ss115946747 Feb 14, 2009 (130)
16 ENSEMBL ss134379241 Dec 01, 2009 (131)
17 ENSEMBL ss143476515 Dec 01, 2009 (131)
18 GMI ss156377612 Dec 01, 2009 (131)
19 COMPLETE_GENOMICS ss162409279 Jul 04, 2010 (132)
20 COMPLETE_GENOMICS ss164673031 Jul 04, 2010 (132)
21 COMPLETE_GENOMICS ss166638306 Jul 04, 2010 (132)
22 BUSHMAN ss199165330 Jul 04, 2010 (132)
23 BCM-HGSC-SUB ss206496698 Jul 04, 2010 (132)
24 1000GENOMES ss223706255 Jul 14, 2010 (132)
25 1000GENOMES ss234438612 Jul 15, 2010 (132)
26 1000GENOMES ss241294637 Jul 15, 2010 (132)
27 BL ss254338733 May 09, 2011 (134)
28 GMI ss279812975 May 04, 2012 (137)
29 GMI ss285844781 Apr 25, 2013 (138)
30 PJP ss294082787 May 09, 2011 (134)
31 TISHKOFF ss560749999 Apr 25, 2013 (138)
32 SSMP ss655187308 Apr 25, 2013 (138)
33 EVA-GONL ss985519301 Aug 21, 2014 (142)
34 JMKIDD_LAB ss1075521892 Aug 21, 2014 (142)
35 1000GENOMES ss1329875918 Aug 21, 2014 (142)
36 DDI ss1431512436 Apr 01, 2015 (144)
37 EVA_GENOME_DK ss1582685333 Apr 01, 2015 (144)
38 EVA_DECODE ss1595114169 Apr 01, 2015 (144)
39 EVA_UK10K_ALSPAC ss1620646696 Apr 01, 2015 (144)
40 EVA_UK10K_TWINSUK ss1663640729 Apr 01, 2015 (144)
41 HAMMER_LAB ss1805535523 Sep 08, 2015 (146)
42 WEILL_CORNELL_DGM ss1928806549 Feb 12, 2016 (147)
43 GENOMED ss1970980347 Jul 19, 2016 (147)
44 JJLAB ss2025103586 Sep 14, 2016 (149)
45 USC_VALOUEV ss2153330247 Dec 20, 2016 (150)
46 HUMAN_LONGEVITY ss2303140941 Dec 20, 2016 (150)
47 SYSTEMSBIOZJU ss2627032817 Nov 08, 2017 (151)
48 GRF ss2709098698 Nov 08, 2017 (151)
49 GNOMAD ss2866840360 Nov 08, 2017 (151)
50 SWEGEN ss3003190613 Nov 08, 2017 (151)
51 BIOINF_KMB_FNS_UNIBA ss3026339053 Nov 08, 2017 (151)
52 CSHL ss3348182748 Nov 08, 2017 (151)
53 URBANLAB ss3648916514 Oct 12, 2018 (152)
54 EGCUT_WGS ss3670867590 Jul 13, 2019 (153)
55 EVA_DECODE ss3722026879 Jul 13, 2019 (153)
56 ACPOP ss3735666853 Jul 13, 2019 (153)
57 EVA ss3768007365 Jul 13, 2019 (153)
58 PACBIO ss3786147162 Jul 13, 2019 (153)
59 PACBIO ss3791402980 Jul 13, 2019 (153)
60 PACBIO ss3796284316 Jul 13, 2019 (153)
61 KHV_HUMAN_GENOMES ss3811164235 Jul 13, 2019 (153)
62 EVA ss3831165949 Apr 26, 2020 (154)
63 EVA ss3839092037 Apr 26, 2020 (154)
64 EVA ss3844551421 Apr 26, 2020 (154)
65 SGDP_PRJ ss3869937869 Apr 26, 2020 (154)
66 KRGDB ss3917443131 Apr 26, 2020 (154)
67 KOGIC ss3963886687 Apr 26, 2020 (154)
68 TOPMED ss4786333373 Apr 26, 2021 (155)
69 TOMMO_GENOMICS ss5188737095 Apr 26, 2021 (155)
70 1000G_HIGH_COVERAGE ss5277161481 Oct 16, 2022 (156)
71 HUGCELL_USP ss5473726179 Oct 16, 2022 (156)
72 1000G_HIGH_COVERAGE ss5567541963 Oct 16, 2022 (156)
73 SANFORD_IMAGENETICS ss5645390030 Oct 16, 2022 (156)
74 TOMMO_GENOMICS ss5730809587 Oct 16, 2022 (156)
75 YY_MCH ss5809715540 Oct 16, 2022 (156)
76 EVA ss5830541277 Oct 16, 2022 (156)
77 EVA ss5856376234 Oct 16, 2022 (156)
78 EVA ss5888985380 Oct 16, 2022 (156)
79 EVA ss5974597066 Oct 16, 2022 (156)
80 1000Genomes NC_000008.10 - 54691609 Oct 12, 2018 (152)
81 1000Genomes_30x NC_000008.11 - 53779049 Oct 16, 2022 (156)
82 The Avon Longitudinal Study of Parents and Children NC_000008.10 - 54691609 Oct 12, 2018 (152)
83 Genetic variation in the Estonian population NC_000008.10 - 54691609 Oct 12, 2018 (152)
84 The Danish reference pan genome NC_000008.10 - 54691609 Apr 26, 2020 (154)
85 gnomAD - Genomes NC_000008.11 - 53779049 Apr 26, 2021 (155)
86 Genome of the Netherlands Release 5 NC_000008.10 - 54691609 Apr 26, 2020 (154)
87 HapMap NC_000008.11 - 53779049 Apr 26, 2020 (154)
88 KOREAN population from KRGDB NC_000008.10 - 54691609 Apr 26, 2020 (154)
89 Korean Genome Project NC_000008.11 - 53779049 Apr 26, 2020 (154)
90 Northern Sweden NC_000008.10 - 54691609 Jul 13, 2019 (153)
91 Qatari NC_000008.10 - 54691609 Apr 26, 2020 (154)
92 SGDP_PRJ NC_000008.10 - 54691609 Apr 26, 2020 (154)
93 Siberian NC_000008.10 - 54691609 Apr 26, 2020 (154)
94 8.3KJPN NC_000008.10 - 54691609 Apr 26, 2021 (155)
95 14KJPN NC_000008.11 - 53779049 Oct 16, 2022 (156)
96 TopMed NC_000008.11 - 53779049 Apr 26, 2021 (155)
97 UK 10K study - Twins NC_000008.10 - 54691609 Oct 12, 2018 (152)
98 A Vietnamese Genetic Variation Database NC_000008.10 - 54691609 Jul 13, 2019 (153)
99 ALFA NC_000008.11 - 53779049 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
24620525, ss3917443131 NC_000008.10:54691608:A:C NC_000008.11:53779048:A:C (self)
ss77270369, ss78156064, ss78748943, ss93888205, ss108030518, ss115405416, ss115946747, ss162409279, ss164673031, ss166638306, ss199165330, ss206496698, ss254338733, ss279812975, ss285844781, ss294082787, ss1595114169 NC_000008.9:54854161:A:G NC_000008.11:53779048:A:G (self)
42001105, 23356442, 16605838, 8850271, 10427470, 24620525, 8951718, 10848479, 21954849, 5846601, 46706402, 23356442, 5197401, ss223706255, ss234438612, ss241294637, ss560749999, ss655187308, ss985519301, ss1075521892, ss1329875918, ss1431512436, ss1582685333, ss1620646696, ss1663640729, ss1805535523, ss1928806549, ss1970980347, ss2025103586, ss2153330247, ss2627032817, ss2709098698, ss2866840360, ss3003190613, ss3348182748, ss3670867590, ss3735666853, ss3768007365, ss3786147162, ss3791402980, ss3796284316, ss3831165949, ss3839092037, ss3869937869, ss3917443131, ss5188737095, ss5645390030, ss5830541277, ss5974597066 NC_000008.10:54691608:A:G NC_000008.11:53779048:A:G (self)
55067898, 296186230, 3623746, 20264688, 64646691, 623710933, 12508484906, ss2303140941, ss3026339053, ss3648916514, ss3722026879, ss3811164235, ss3844551421, ss3963886687, ss4786333373, ss5277161481, ss5473726179, ss5567541963, ss5730809587, ss5809715540, ss5856376234, ss5888985380 NC_000008.11:53779048:A:G NC_000008.11:53779048:A:G (self)
ss10484563, ss11967479 NT_008183.16:6534156:A:G NC_000008.11:53779048:A:G (self)
ss14337538, ss14526133, ss17232397 NT_008183.17:6534156:A:G NC_000008.11:53779048:A:G (self)
ss44856924, ss97873704, ss105618722, ss134379241, ss143476515, ss156377612 NT_008183.19:6556009:A:G NC_000008.11:53779048:A:G (self)
24620525, ss3917443131 NC_000008.10:54691608:A:T NC_000008.11:53779048:A:T (self)
12508484906 NC_000008.11:53779048:A:T NC_000008.11:53779048:A:T (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 rs6473891

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