Name: rs17853498
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.

rs17853498

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr2:70935981 (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>C
Variation Type: SNV Single Nucleotide Variation
Frequency: C=0.114485 (30303/264690, TOPMED)
C=0.117839 (29531/250604, GnomAD_exome)
C=0.115273 (16147/140076, GnomAD) (+ 20 more)
C=0.121538 (14622/120308, ExAC)
C=0.06998 (3262/46616, ALFA)
C=0.15277 (4317/28258, 14KJPN)
C=0.15149 (2539/16760, 8.3KJPN)
C=0.11026 (1434/13006, GO-ESP)
C=0.1674 (1072/6404, 1000G_30x)
C=0.1711 (857/5008, 1000G)
C=0.0786 (352/4478, Estonian)
C=0.0911 (351/3854, ALSPAC)
C=0.0944 (350/3708, TWINSUK)
C=0.1986 (580/2920, KOREAN)
C=0.1885 (345/1830, Korea1K)
C=0.248 (151/608, Vietnamese)
C=0.102 (61/600, NorthernSweden)
C=0.115 (35/304, FINRISK)
C=0.120 (26/216, Qatari)
T=0.493 (70/142, SGDP_PRJ)
C=0.10 (4/40, GENOME_DK)
T=0.50 (8/16, Siberian)
C=0.50 (8/16, Siberian)

Clinical Significance: Reported in ClinVar
Gene : Consequence: ATP6V1B1 : Synonymous Variant
Publications: 2 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	62976	T=0.92003	C=0.07997
European	Sub	45756	T=0.92709	C=0.07291
African	Sub	7622	T=0.8797	C=0.1203
African Others	Sub	282	T=0.876	C=0.124
African American	Sub	7340	T=0.8798	C=0.1202
Asian	Sub	130	T=0.908	C=0.092
East Asian	Sub	86	T=0.93	C=0.07
Other Asian	Sub	44	T=0.86	C=0.14
Latin American 1	Sub	480	T=0.919	C=0.081
Latin American 2	Sub	546	T=0.991	C=0.009
South Asian	Sub	66	T=1.00	C=0.00
Other	Sub	8376	T=0.9132	C=0.0868

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").

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Study	Population	Group	Sample Size	Ref Allele	Alt Allele
TopMed	Global	Study-wide	264690	T=0.885515	C=0.114485
gnomAD - Exomes	Global	Study-wide	250604	T=0.882161	C=0.117839
gnomAD - Exomes	European	Sub	134856	T=0.909244	C=0.090756
gnomAD - Exomes	Asian	Sub	48956	T=0.77913	C=0.22087
gnomAD - Exomes	American	Sub	34498	T=0.94313	C=0.05687
gnomAD - Exomes	African	Sub	16154	T=0.83385	C=0.16615
gnomAD - Exomes	Ashkenazi Jewish	Sub	10036	T=0.88312	C=0.11688
gnomAD - Exomes	Other	Sub	6104	T=0.8919	C=0.1081
gnomAD - Genomes	Global	Study-wide	140076	T=0.884727	C=0.115273
gnomAD - Genomes	European	Sub	75890	T=0.90733	C=0.09267
gnomAD - Genomes	African	Sub	41942	T=0.84138	C=0.15862
gnomAD - Genomes	American	Sub	13646	T=0.92203	C=0.07797
gnomAD - Genomes	Ashkenazi Jewish	Sub	3320	T=0.8807	C=0.1193
gnomAD - Genomes	East Asian	Sub	3128	T=0.7561	C=0.2439
gnomAD - Genomes	Other	Sub	2150	T=0.8893	C=0.1107
ExAC	Global	Study-wide	120308	T=0.878462	C=0.121538
ExAC	Europe	Sub	72608	T=0.90734	C=0.09266
ExAC	Asian	Sub	24998	T=0.78490	C=0.21510
ExAC	American	Sub	11536	T=0.94235	C=0.05765
ExAC	African	Sub	10272	T=0.82973	C=0.17027
ExAC	Other	Sub	894	T=0.885	C=0.115
Allele Frequency Aggregator	Total	Global	46616	T=0.93002	C=0.06998
Allele Frequency Aggregator	European	Sub	35668	T=0.92977	C=0.07023
Allele Frequency Aggregator	Other	Sub	6942	T=0.9144	C=0.0856
Allele Frequency Aggregator	African	Sub	2784	T=0.9616	C=0.0384
Allele Frequency Aggregator	Latin American 2	Sub	546	T=0.991	C=0.009
Allele Frequency Aggregator	Latin American 1	Sub	480	T=0.919	C=0.081
Allele Frequency Aggregator	Asian	Sub	130	T=0.908	C=0.092
Allele Frequency Aggregator	South Asian	Sub	66	T=1.00	C=0.00
14KJPN	JAPANESE	Study-wide	28258	T=0.84723	C=0.15277
8.3KJPN	JAPANESE	Study-wide	16760	T=0.84851	C=0.15149
GO Exome Sequencing Project	Global	Study-wide	13006	T=0.88974	C=0.11026
GO Exome Sequencing Project	European American	Sub	8600	T=0.9129	C=0.0871
GO Exome Sequencing Project	African American	Sub	4406	T=0.8445	C=0.1555
1000Genomes_30x	Global	Study-wide	6404	T=0.8326	C=0.1674
1000Genomes_30x	African	Sub	1786	T=0.7956	C=0.2044
1000Genomes_30x	Europe	Sub	1266	T=0.8910	C=0.1090
1000Genomes_30x	South Asian	Sub	1202	T=0.7903	C=0.2097
1000Genomes_30x	East Asian	Sub	1170	T=0.7872	C=0.2128
1000Genomes_30x	American	Sub	980	T=0.931	C=0.069
1000Genomes	Global	Study-wide	5008	T=0.8289	C=0.1711
1000Genomes	African	Sub	1322	T=0.7890	C=0.2110
1000Genomes	East Asian	Sub	1008	T=0.7927	C=0.2073
1000Genomes	Europe	Sub	1006	T=0.8887	C=0.1113
1000Genomes	South Asian	Sub	978	T=0.788	C=0.212
1000Genomes	American	Sub	694	T=0.928	C=0.072
Genetic variation in the Estonian population	Estonian	Study-wide	4478	T=0.9214	C=0.0786
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.9089	C=0.0911
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.9056	C=0.0944
KOREAN population from KRGDB	KOREAN	Study-wide	2920	T=0.8014	C=0.1986
Korean Genome Project	KOREAN	Study-wide	1830	T=0.8115	C=0.1885
A Vietnamese Genetic Variation Database	Global	Study-wide	608	T=0.752	C=0.248
Northern Sweden	ACPOP	Study-wide	600	T=0.898	C=0.102
FINRISK	Finnish from FINRISK project	Study-wide	304	T=0.885	C=0.115
Qatari	Global	Study-wide	216	T=0.880	C=0.120
SGDP_PRJ	Global	Study-wide	142	T=0.493	C=0.507
The Danish reference pan genome	Danish	Study-wide	40	T=0.90	C=0.10
Siberian	Global	Study-wide	16	T=0.50	C=0.50

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 2	NC_000002.12:g.70935981T>C
GRCh37.p13 chr 2	NC_000002.11:g.71163111T>C
ATP6V1B1 RefSeqGene (LRG_1176)	NG_008016.1:g.5114T>C
GRCh37.p13 chr 2 fix patch HG953_PATCH	NW_004504299.1:g.502262T>C

Gene: ATP6V1B1, ATPase H+ transporting V1 subunit B1 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
ATP6V1B1 transcript	NM_001692.4:c.27T>C	P [CCT] > P [CCC]	Coding Sequence Variant
V-type proton ATPase subunit B, kidney isoform	NP_001683.2:p.Pro9=	P (Pro) > P (Pro)	Synonymous Variant
ATP6V1B1 transcript variant X1	XM_011532907.3:c.	N/A	Genic Upstream Transcript 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.

Allele: C (allele ID: 53394 )

ClinVar Accession	Disease Names	Clinical Significance
RCV000037206.8	not specified	Benign
RCV000404834.6	Renal tubular acidosis with progressive nerve deafness	Benign
RCV001522716.4	not provided	Benign

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=	C
GRCh38.p14 chr 2	NC_000002.12:g.70935981=	NC_000002.12:g.70935981T>C
GRCh37.p13 chr 2	NC_000002.11:g.71163111=	NC_000002.11:g.71163111T>C
ATP6V1B1 RefSeqGene (LRG_1176)	NG_008016.1:g.5114=	NG_008016.1:g.5114T>C
ATP6V1B1 transcript	NM_001692.4:c.27=	NM_001692.4:c.27T>C
ATP6V1B1 transcript	NM_001692.3:c.27=	NM_001692.3:c.27T>C
GRCh37.p13 chr 2 fix patch HG953_PATCH	NW_004504299.1:g.502262=	NW_004504299.1:g.502262T>C
V-type proton ATPase subunit B, kidney isoform	NP_001683.2:p.Pro9=	NP_001683.2:p.Pro9=

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#.

71 SubSNP, 22 Frequency, 3 ClinVar submissions

No	Submitter	Submission ID	Date (Build)
1	MGC_GENOME_DIFF	ss28507800	Sep 24, 2004 (123)
2	GMI	ss157207095	Dec 01, 2009 (131)
3	SEATTLESEQ	ss159702125	Dec 01, 2009 (131)
4	BUSHMAN	ss200605910	Jul 04, 2010 (132)
5	1000GENOMES	ss219317871	Jul 14, 2010 (132)
6	1000GENOMES	ss231220993	Jul 14, 2010 (132)
7	1000GENOMES	ss238763783	Jul 15, 2010 (132)
8	GMI	ss276519295	May 04, 2012 (137)
9	NHLBI-ESP	ss342064293	May 09, 2011 (134)
10	1000GENOMES	ss489819976	May 04, 2012 (137)
11	CLINSEQ_SNP	ss491784838	May 04, 2012 (137)
12	ILLUMINA	ss536509832	Sep 11, 2015 (146)
13	SSMP	ss649239005	Apr 25, 2013 (138)
14	JMKIDD_LAB	ss974442564	Aug 21, 2014 (142)
15	EVA-GONL	ss976974372	Aug 21, 2014 (142)
16	JMKIDD_LAB	ss1067438089	Aug 21, 2014 (142)
17	JMKIDD_LAB	ss1069221365	Aug 21, 2014 (142)
18	1000GENOMES	ss1297774849	Aug 21, 2014 (142)
19	DDI	ss1428618249	Apr 09, 2015 (144)
20	EVA_GENOME_DK	ss1578935453	Apr 09, 2015 (144)
21	EVA_FINRISK	ss1584019078	Apr 09, 2015 (144)
22	EVA_DECODE	ss1586390888	Apr 01, 2015 (144)
23	EVA_UK10K_ALSPAC	ss1603805205	Apr 09, 2015 (144)
24	EVA_UK10K_TWINSUK	ss1646799238	Apr 09, 2015 (144)
25	EVA_EXAC	ss1686349131	Apr 09, 2015 (144)
26	HAMMER_LAB	ss1796933037	Sep 11, 2015 (146)
27	WEILL_CORNELL_DGM	ss1920202301	Feb 17, 2016 (147)
28	JJLAB	ss2020635564	Sep 28, 2016 (149)
29	USC_VALOUEV	ss2148682092	Oct 11, 2018 (152)
30	HUMAN_LONGEVITY	ss2231428074	Dec 20, 2016 (150)
31	SYSTEMSBIOZJU	ss2624828500	Oct 11, 2018 (152)
32	GRF	ss2703255271	Oct 11, 2018 (152)
33	GNOMAD	ss2732729614	Oct 11, 2018 (152)
34	GNOMAD	ss2746699408	Oct 11, 2018 (152)
35	GNOMAD	ss2775010822	Oct 11, 2018 (152)
36	SWEGEN	ss2989716843	Oct 11, 2018 (152)
37	CSHL	ss3344288358	Oct 11, 2018 (152)
38	BIOINF_KMB_FNS_UNIBA	ss3645559465	Oct 11, 2018 (152)
39	OMUKHERJEE_ADBS	ss3646262346	Oct 11, 2018 (152)
40	EGCUT_WGS	ss3657697812	Jul 13, 2019 (153)
41	EVA_DECODE	ss3704151229	Jul 13, 2019 (153)
42	ACPOP	ss3728545359	Jul 13, 2019 (153)
43	EVA	ss3756921306	Jul 13, 2019 (153)
44	KHV_HUMAN_GENOMES	ss3801289637	Jul 13, 2019 (153)
45	EVA	ss3823778143	Apr 25, 2020 (154)
46	EVA	ss3825602545	Apr 25, 2020 (154)
47	SGDP_PRJ	ss3852537960	Apr 25, 2020 (154)
48	KRGDB	ss3897958633	Apr 25, 2020 (154)
49	KOGIC	ss3948011126	Apr 25, 2020 (154)
50	FSA-LAB	ss3984178957	Apr 26, 2021 (155)
51	FSA-LAB	ss3984178958	Apr 26, 2021 (155)
52	EVA	ss3986184381	Apr 26, 2021 (155)
53	GNOMAD	ss4043649544	Apr 26, 2021 (155)
54	TOPMED	ss4510459446	Apr 26, 2021 (155)
55	TOMMO_GENOMICS	ss5151962994	Apr 26, 2021 (155)
56	EVA	ss5236971154	Apr 26, 2021 (155)
57	EVA	ss5237635818	Oct 12, 2022 (156)
58	1000G_HIGH_COVERAGE	ss5248519895	Oct 12, 2022 (156)
59	TRAN_CS_UWATERLOO	ss5314401497	Oct 12, 2022 (156)
60	EVA	ss5329776428	Oct 12, 2022 (156)
61	HUGCELL_USP	ss5448680523	Oct 12, 2022 (156)
62	1000G_HIGH_COVERAGE	ss5523981169	Oct 12, 2022 (156)
63	SANFORD_IMAGENETICS	ss5628999121	Oct 12, 2022 (156)
64	TOMMO_GENOMICS	ss5680759566	Oct 12, 2022 (156)
65	YY_MCH	ss5802314733	Oct 12, 2022 (156)
66	EVA	ss5820275400	Oct 12, 2022 (156)
67	EVA	ss5848516181	Oct 12, 2022 (156)
68	EVA	ss5852573594	Oct 12, 2022 (156)
69	EVA	ss5930899486	Oct 12, 2022 (156)
70	EVA	ss5955245423	Oct 12, 2022 (156)
71	EVA	ss5981205372	Oct 12, 2022 (156)
72	1000Genomes	NC_000002.11 - 71163111	Oct 11, 2018 (152)
73	1000Genomes_30x	NC_000002.12 - 70935981	Oct 12, 2022 (156)
74	The Avon Longitudinal Study of Parents and Children	NC_000002.11 - 71163111	Oct 11, 2018 (152)
75	Genetic variation in the Estonian population	NC_000002.11 - 71163111	Oct 11, 2018 (152)
76	ExAC	NC_000002.11 - 71163111	Oct 11, 2018 (152)
77	FINRISK	NC_000002.11 - 71163111	Apr 25, 2020 (154)
78	The Danish reference pan genome	NC_000002.11 - 71163111	Apr 25, 2020 (154)
79	gnomAD - Genomes	NC_000002.12 - 70935981	Apr 26, 2021 (155)
80	gnomAD - Exomes	NC_000002.11 - 71163111	Jul 13, 2019 (153)
81	GO Exome Sequencing Project	NC_000002.11 - 71163111	Oct 11, 2018 (152)
82	KOREAN population from KRGDB	NC_000002.11 - 71163111	Apr 25, 2020 (154)
83	Korean Genome Project	NC_000002.12 - 70935981	Apr 25, 2020 (154)
84	Northern Sweden	NC_000002.11 - 71163111	Jul 13, 2019 (153)
85	Qatari	NC_000002.11 - 71163111	Apr 25, 2020 (154)
86	SGDP_PRJ	NC_000002.11 - 71163111	Apr 25, 2020 (154)
87	Siberian	NC_000002.11 - 71163111	Apr 25, 2020 (154)
88	8.3KJPN	NC_000002.11 - 71163111	Apr 26, 2021 (155)
89	14KJPN	NC_000002.12 - 70935981	Oct 12, 2022 (156)
90	TopMed	NC_000002.12 - 70935981	Apr 26, 2021 (155)
91	UK 10K study - Twins	NC_000002.11 - 71163111	Oct 11, 2018 (152)
92	A Vietnamese Genetic Variation Database	NC_000002.11 - 71163111	Jul 13, 2019 (153)
93	ALFA	NC_000002.12 - 70935981	Apr 26, 2021 (155)
94	ClinVar	RCV000037206.8	Oct 12, 2022 (156)
95	ClinVar	RCV000404834.6	Oct 12, 2022 (156)
96	ClinVar	RCV001522716.4	Oct 12, 2022 (156)

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
ss200605910, ss276519295, ss491784838, ss1586390888	NC_000002.10:71016618:T:C	NC_000002.12:70935980:T:C	(self)
8737573, 4862362, 3436060, 6223136, 15539, 5105456, 1781634, 236603, 5136027, 1830224, 2244231, 4554940, 1198446, 9932301, 4862362, 1054127, ss219317871, ss231220993, ss238763783, ss342064293, ss489819976, ss536509832, ss649239005, ss974442564, ss976974372, ss1067438089, ss1069221365, ss1297774849, ss1428618249, ss1578935453, ss1584019078, ss1603805205, ss1646799238, ss1686349131, ss1796933037, ss1920202301, ss2020635564, ss2148682092, ss2624828500, ss2703255271, ss2732729614, ss2746699408, ss2775010822, ss2989716843, ss3344288358, ss3646262346, ss3657697812, ss3728545359, ss3756921306, ss3823778143, ss3825602545, ss3852537960, ss3897958633, ss3984178957, ss3984178958, ss3986184381, ss5151962994, ss5329776428, ss5628999121, ss5820275400, ss5848516181, ss5955245423, ss5981205372	NC_000002.11:71163110:T:C	NC_000002.12:70935980:T:C	(self)
RCV000037206.8, RCV000404834.6, RCV001522716.4, 11507104, 62045521, 4389127, 14596670, 314282325, 7602462106, ss2231428074, ss3645559465, ss3704151229, ss3801289637, ss3948011126, ss4043649544, ss4510459446, ss5236971154, ss5237635818, ss5248519895, ss5314401497, ss5448680523, ss5523981169, ss5680759566, ss5802314733, ss5852573594, ss5930899486	NC_000002.12:70935980:T:C	NC_000002.12:70935980:T:C	(self)
ss28507800, ss157207095, ss159702125	NT_022184.15:49984997:T:C	NC_000002.12:70935980:T:C	(self)

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

2 citations for rs17853498

PMID	Title	Author	Year	Journal
24033266	A systematic approach to assessing the clinical significance of genetic variants.	Duzkale H et al.	2013	Clinical genetics
27767102	A single nucleotide polymorphism in kidney anion exchanger 1 gene is associated with incomplete type 1 renal tubular acidosis.	Takeuchi T et al.	2016	Scientific reports

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.

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dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs17853498