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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.

rs1543922

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr19:51581583 (GRCh38.p13) 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
C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.121750 (32226/264690, TOPMED)
T=0.026543 (6377/240256, ALFA)
T=0.114621 (16058/140096, GnomAD) (+ 20 more)
T=0.19495 (15341/78692, PAGE_STUDY)
T=0.16008 (2683/16760, 8.3KJPN)
T=0.1400 (701/5008, 1000G)
T=0.0145 (65/4480, Estonian)
T=0.0052 (20/3854, ALSPAC)
T=0.0065 (24/3708, TWINSUK)
T=0.1547 (452/2922, KOREAN)
T=0.1017 (212/2084, HGDP_Stanford)
T=0.1583 (290/1832, Korea1K)
T=0.1691 (302/1786, HapMap)
T=0.006 (6/998, GoNL)
T=0.141 (111/790, PRJEB37584)
T=0.017 (10/600, NorthernSweden)
T=0.007 (4/534, MGP)
T=0.065 (14/216, Qatari)
T=0.090 (19/212, Vietnamese)
C=0.421 (48/114, SGDP_PRJ)
T=0.00 (0/78, Ancient Sardinia)
T=0.03 (1/40, GENOME_DK)
C=0.33 (8/24, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
ZNF175 : Intron Variant
Publications
0 citations
Genomic View
See rs on genome
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.p13 chr 19 NC_000019.10:g.51581583C>T
GRCh37.p13 chr 19 NC_000019.9:g.52084836C>T
Gene: ZNF175, zinc finger protein 175 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
ZNF175 transcript variant 1 NM_007147.4:c.199+66C>T N/A Intron Variant
ZNF175 transcript variant 2 NR_136208.2:n. N/A Genic Downstream Transcript Variant
ZNF175 transcript variant X1 XM_017027249.2:c.34+66C>T 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

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: 20201027095038
Population Group Sample Size Ref Allele Alt Allele
Total Global 240256 C=0.973457 T=0.026543
European Sub 211836 C=0.990785 T=0.009215
African Sub 7956 C=0.6843 T=0.3157
African Others Sub 296 C=0.672 T=0.328
African American Sub 7660 C=0.6847 T=0.3153
Asian Sub 3868 C=0.8294 T=0.1706
East Asian Sub 3136 C=0.8527 T=0.1473
Other Asian Sub 732 C=0.730 T=0.270
Latin American 1 Sub 1042 C=0.8877 T=0.1123
Latin American 2 Sub 6648 C=0.9117 T=0.0883
South Asian Sub 366 C=0.978 T=0.022
Other Sub 8540 C=0.9367 T=0.0633


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 C=0.878250 T=0.121750
gnomAD - Genomes Global Study-wide 140096 C=0.885379 T=0.114621
gnomAD - Genomes European Sub 75920 C=0.98676 T=0.01324
gnomAD - Genomes African Sub 41922 C=0.68742 T=0.31258
gnomAD - Genomes American Sub 13654 C=0.90669 T=0.09331
gnomAD - Genomes Ashkenazi Jewish Sub 3322 C=0.9928 T=0.0072
gnomAD - Genomes East Asian Sub 3132 C=0.8608 T=0.1392
gnomAD - Genomes Other Sub 2146 C=0.8998 T=0.1002
The PAGE Study Global Study-wide 78692 C=0.80505 T=0.19495
The PAGE Study AfricanAmerican Sub 32512 C=0.69605 T=0.30395
The PAGE Study Mexican Sub 10810 C=0.92442 T=0.07558
The PAGE Study Asian Sub 8316 C=0.8321 T=0.1679
The PAGE Study PuertoRican Sub 7918 C=0.8849 T=0.1151
The PAGE Study NativeHawaiian Sub 4530 C=0.8382 T=0.1618
The PAGE Study Cuban Sub 4230 C=0.9383 T=0.0617
The PAGE Study Dominican Sub 3828 C=0.8339 T=0.1661
The PAGE Study CentralAmerican Sub 2450 C=0.8547 T=0.1453
The PAGE Study SouthAmerican Sub 1982 C=0.8860 T=0.1140
The PAGE Study NativeAmerican Sub 1260 C=0.9222 T=0.0778
The PAGE Study SouthAsian Sub 856 C=0.971 T=0.029
8.3KJPN JAPANESE Study-wide 16760 C=0.83992 T=0.16008
1000Genomes Global Study-wide 5008 C=0.8600 T=0.1400
1000Genomes African Sub 1322 C=0.6513 T=0.3487
1000Genomes East Asian Sub 1008 C=0.8790 T=0.1210
1000Genomes Europe Sub 1006 C=0.9881 T=0.0119
1000Genomes South Asian Sub 978 C=0.969 T=0.031
1000Genomes American Sub 694 C=0.890 T=0.110
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.9855 T=0.0145
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.9948 T=0.0052
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.9935 T=0.0065
KOREAN population from KRGDB KOREAN Study-wide 2922 C=0.8453 T=0.1547
HGDP-CEPH-db Supplement 1 Global Study-wide 2084 C=0.8983 T=0.1017
HGDP-CEPH-db Supplement 1 Est_Asia Sub 470 C=0.811 T=0.189
HGDP-CEPH-db Supplement 1 Central_South_Asia Sub 414 C=0.961 T=0.039
HGDP-CEPH-db Supplement 1 Middle_Est Sub 350 C=0.937 T=0.063
HGDP-CEPH-db Supplement 1 Europe Sub 320 C=0.991 T=0.009
HGDP-CEPH-db Supplement 1 Africa Sub 242 C=0.748 T=0.252
HGDP-CEPH-db Supplement 1 America Sub 216 C=0.921 T=0.079
HGDP-CEPH-db Supplement 1 Oceania Sub 72 C=0.94 T=0.06
Korean Genome Project KOREAN Study-wide 1832 C=0.8417 T=0.1583
HapMap Global Study-wide 1786 C=0.8309 T=0.1691
HapMap African Sub 692 C=0.705 T=0.295
HapMap American Sub 664 C=0.905 T=0.095
HapMap Asian Sub 254 C=0.866 T=0.134
HapMap Europe Sub 176 C=0.994 T=0.006
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 C=0.994 T=0.006
CNV burdens in cranial meningiomas Global Study-wide 790 C=0.859 T=0.141
CNV burdens in cranial meningiomas CRM Sub 790 C=0.859 T=0.141
Northern Sweden ACPOP Study-wide 600 C=0.983 T=0.017
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 C=0.993 T=0.007
Qatari Global Study-wide 216 C=0.935 T=0.065
A Vietnamese Genetic Variation Database Global Study-wide 212 C=0.910 T=0.090
SGDP_PRJ Global Study-wide 114 C=0.421 T=0.579
Ancient Sardinia genome-wide 1240k capture data generation and analysis Global Study-wide 78 C=1.00 T=0.00
The Danish reference pan genome Danish Study-wide 40 C=0.97 T=0.03
Siberian Global Study-wide 24 C=0.33 T=0.67
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 C= T
GRCh38.p13 chr 19 NC_000019.10:g.51581583= NC_000019.10:g.51581583C>T
GRCh37.p13 chr 19 NC_000019.9:g.52084836= NC_000019.9:g.52084836C>T
ZNF175 transcript NM_007147.2:c.199+66= NM_007147.2:c.199+66C>T
ZNF175 transcript variant 1 NM_007147.4:c.199+66= NM_007147.4:c.199+66C>T
ZNF175 transcript variant X2 XM_005259217.1:c.199+66= XM_005259217.1:c.199+66C>T
ZNF175 transcript variant X3 XM_005259218.1:c.199+66= XM_005259218.1:c.199+66C>T
ZNF175 transcript variant X1 XM_017027249.2:c.34+66= XM_017027249.2:c.34+66C>T
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#.

93 SubSNP, 23 Frequency submissions
No Submitter Submission ID Date (Build)
1 TSC-CSHL ss2386045 Oct 23, 2000 (88)
2 SC_JCM ss5971142 Feb 20, 2003 (111)
3 PERLEGEN ss23767064 Sep 20, 2004 (123)
4 ABI ss44192276 Mar 14, 2006 (126)
5 AFFY ss66001567 Nov 29, 2006 (127)
6 ILLUMINA ss67469070 Nov 29, 2006 (127)
7 ILLUMINA ss71180732 May 16, 2007 (127)
8 ILLUMINA ss75376733 Dec 06, 2007 (129)
9 ILLUMINA-UK ss117732810 Feb 14, 2009 (130)
10 KRIBB_YJKIM ss119397739 Dec 01, 2009 (131)
11 ILLUMINA ss160369949 Dec 01, 2009 (131)
12 ILLUMINA ss172570295 Jul 04, 2010 (132)
13 1000GENOMES ss228180464 Jul 14, 2010 (132)
14 1000GENOMES ss243905900 Jul 15, 2010 (132)
15 GMI ss283242144 May 04, 2012 (137)
16 ILLUMINA ss480025273 May 04, 2012 (137)
17 ILLUMINA ss480034089 May 04, 2012 (137)
18 ILLUMINA ss480697229 Sep 08, 2015 (146)
19 ILLUMINA ss484810829 May 04, 2012 (137)
20 ILLUMINA ss536891020 Sep 08, 2015 (146)
21 TISHKOFF ss566040785 Apr 25, 2013 (138)
22 SSMP ss661907461 Apr 25, 2013 (138)
23 ILLUMINA ss778812300 Sep 08, 2015 (146)
24 ILLUMINA ss782851977 Sep 08, 2015 (146)
25 ILLUMINA ss783816497 Sep 08, 2015 (146)
26 ILLUMINA ss832105867 Sep 08, 2015 (146)
27 ILLUMINA ss834272572 Sep 08, 2015 (146)
28 EVA-GONL ss994391452 Aug 21, 2014 (142)
29 JMKIDD_LAB ss1081965823 Aug 21, 2014 (142)
30 1000GENOMES ss1363531961 Aug 21, 2014 (142)
31 EVA_GENOME_DK ss1578674340 Apr 01, 2015 (144)
32 EVA_UK10K_ALSPAC ss1638138957 Apr 01, 2015 (144)
33 EVA_UK10K_TWINSUK ss1681132990 Apr 01, 2015 (144)
34 EVA_DECODE ss1698446168 Apr 01, 2015 (144)
35 EVA_MGP ss1711522994 Apr 01, 2015 (144)
36 EVA_SVP ss1713668209 Apr 01, 2015 (144)
37 ILLUMINA ss1752292731 Sep 08, 2015 (146)
38 HAMMER_LAB ss1809351034 Sep 08, 2015 (146)
39 WEILL_CORNELL_DGM ss1937893221 Feb 12, 2016 (147)
40 ILLUMINA ss1946540689 Feb 12, 2016 (147)
41 ILLUMINA ss1959878451 Feb 12, 2016 (147)
42 GENOMED ss1968659103 Jul 19, 2016 (147)
43 JJLAB ss2029721631 Sep 14, 2016 (149)
44 ILLUMINA ss2095086073 Dec 20, 2016 (150)
45 USC_VALOUEV ss2158271179 Dec 20, 2016 (150)
46 HUMAN_LONGEVITY ss2226421951 Dec 20, 2016 (150)
47 TOPMED ss2392261149 Dec 20, 2016 (150)
48 ILLUMINA ss2633551179 Nov 08, 2017 (151)
49 GRF ss2702884067 Nov 08, 2017 (151)
50 ILLUMINA ss2710885784 Nov 08, 2017 (151)
51 GNOMAD ss2963937847 Nov 08, 2017 (151)
52 SWEGEN ss3017633034 Nov 08, 2017 (151)
53 ILLUMINA ss3021920249 Nov 08, 2017 (151)
54 TOPMED ss3295697836 Nov 08, 2017 (151)
55 CSHL ss3352346083 Nov 08, 2017 (151)
56 ILLUMINA ss3625744470 Oct 12, 2018 (152)
57 ILLUMINA ss3627955544 Oct 12, 2018 (152)
58 ILLUMINA ss3631521540 Oct 12, 2018 (152)
59 ILLUMINA ss3633183298 Oct 12, 2018 (152)
60 ILLUMINA ss3633894068 Oct 12, 2018 (152)
61 ILLUMINA ss3634742380 Oct 12, 2018 (152)
62 ILLUMINA ss3635580753 Oct 12, 2018 (152)
63 ILLUMINA ss3636428630 Oct 12, 2018 (152)
64 ILLUMINA ss3637332525 Oct 12, 2018 (152)
65 ILLUMINA ss3638233792 Oct 12, 2018 (152)
66 ILLUMINA ss3640449686 Oct 12, 2018 (152)
67 ILLUMINA ss3643205923 Oct 12, 2018 (152)
68 ILLUMINA ss3644729230 Oct 12, 2018 (152)
69 ILLUMINA ss3652347141 Oct 12, 2018 (152)
70 EGCUT_WGS ss3684368156 Jul 13, 2019 (153)
71 EVA_DECODE ss3702954325 Jul 13, 2019 (153)
72 ILLUMINA ss3725740679 Jul 13, 2019 (153)
73 ACPOP ss3743119558 Jul 13, 2019 (153)
74 ILLUMINA ss3744168177 Jul 13, 2019 (153)
75 ILLUMINA ss3745042376 Jul 13, 2019 (153)
76 EVA ss3756171857 Jul 13, 2019 (153)
77 PAGE_CC ss3772022965 Jul 13, 2019 (153)
78 ILLUMINA ss3772539379 Jul 13, 2019 (153)
79 KHV_HUMAN_GENOMES ss3821422800 Jul 13, 2019 (153)
80 EVA ss3825942629 Apr 27, 2020 (154)
81 HGDP ss3847601781 Apr 27, 2020 (154)
82 SGDP_PRJ ss3888423635 Apr 27, 2020 (154)
83 KRGDB ss3938579966 Apr 27, 2020 (154)
84 KOGIC ss3981565061 Apr 27, 2020 (154)
85 FSA-LAB ss3984161426 Apr 26, 2021 (155)
86 EVA ss3984743998 Apr 26, 2021 (155)
87 EVA ss3985858685 Apr 26, 2021 (155)
88 EVA ss3986811044 Apr 26, 2021 (155)
89 EVA ss4017829872 Apr 26, 2021 (155)
90 TOPMED ss5077870913 Apr 26, 2021 (155)
91 TOMMO_GENOMICS ss5228212608 Apr 26, 2021 (155)
92 EVA ss5237249045 Apr 26, 2021 (155)
93 EVA ss5237598943 Apr 26, 2021 (155)
94 1000Genomes NC_000019.9 - 52084836 Oct 12, 2018 (152)
95 The Avon Longitudinal Study of Parents and Children NC_000019.9 - 52084836 Oct 12, 2018 (152)
96 Genetic variation in the Estonian population NC_000019.9 - 52084836 Oct 12, 2018 (152)
97 The Danish reference pan genome NC_000019.9 - 52084836 Apr 27, 2020 (154)
98 gnomAD - Genomes NC_000019.10 - 51581583 Apr 26, 2021 (155)
99 Genome of the Netherlands Release 5 NC_000019.9 - 52084836 Apr 27, 2020 (154)
100 HGDP-CEPH-db Supplement 1 NC_000019.8 - 56776648 Apr 27, 2020 (154)
101 HapMap NC_000019.10 - 51581583 Apr 27, 2020 (154)
102 KOREAN population from KRGDB NC_000019.9 - 52084836 Apr 27, 2020 (154)
103 Korean Genome Project NC_000019.10 - 51581583 Apr 27, 2020 (154)
104 Medical Genome Project healthy controls from Spanish population NC_000019.9 - 52084836 Apr 27, 2020 (154)
105 Northern Sweden NC_000019.9 - 52084836 Jul 13, 2019 (153)
106 The PAGE Study NC_000019.10 - 51581583 Jul 13, 2019 (153)
107 Ancient Sardinia genome-wide 1240k capture data generation and analysis NC_000019.9 - 52084836 Apr 26, 2021 (155)
108 CNV burdens in cranial meningiomas NC_000019.9 - 52084836 Apr 26, 2021 (155)
109 Qatari NC_000019.9 - 52084836 Apr 27, 2020 (154)
110 SGDP_PRJ NC_000019.9 - 52084836 Apr 27, 2020 (154)
111 Siberian NC_000019.9 - 52084836 Apr 27, 2020 (154)
112 8.3KJPN NC_000019.9 - 52084836 Apr 26, 2021 (155)
113 TopMed NC_000019.10 - 51581583 Apr 26, 2021 (155)
114 UK 10K study - Twins NC_000019.9 - 52084836 Oct 12, 2018 (152)
115 A Vietnamese Genetic Variation Database NC_000019.9 - 52084836 Jul 13, 2019 (153)
116 ALFA NC_000019.10 - 51581583 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
279673, ss117732810, ss283242144, ss480025273, ss1698446168, ss1713668209, ss3643205923, ss3847601781 NC_000019.8:56776647:C:T NC_000019.10:51581582:C:T (self)
76952442, 42601342, 30106404, 4855440, 18977544, 45757360, 638754, 16404423, 1084612, 293560, 19935143, 40440615, 10787533, 86181915, 42601342, 9404811, ss228180464, ss243905900, ss480034089, ss480697229, ss484810829, ss536891020, ss566040785, ss661907461, ss778812300, ss782851977, ss783816497, ss832105867, ss834272572, ss994391452, ss1081965823, ss1363531961, ss1578674340, ss1638138957, ss1681132990, ss1711522994, ss1752292731, ss1809351034, ss1937893221, ss1946540689, ss1959878451, ss1968659103, ss2029721631, ss2095086073, ss2158271179, ss2392261149, ss2633551179, ss2702884067, ss2710885784, ss2963937847, ss3017633034, ss3021920249, ss3352346083, ss3625744470, ss3627955544, ss3631521540, ss3633183298, ss3633894068, ss3634742380, ss3635580753, ss3636428630, ss3637332525, ss3638233792, ss3640449686, ss3644729230, ss3652347141, ss3684368156, ss3743119558, ss3744168177, ss3745042376, ss3756171857, ss3772539379, ss3825942629, ss3888423635, ss3938579966, ss3984161426, ss3984743998, ss3985858685, ss3986811044, ss4017829872, ss5228212608, ss5237598943 NC_000019.9:52084835:C:T NC_000019.10:51581582:C:T (self)
542707224, 1709375, 37943062, 1244434, 183031003, 293416577, 6943933165, ss2226421951, ss3295697836, ss3702954325, ss3725740679, ss3772022965, ss3821422800, ss3981565061, ss5077870913, ss5237249045 NC_000019.10:51581582:C:T NC_000019.10:51581582:C:T (self)
ss2386045, ss5971142, ss23767064, ss44192276, ss66001567, ss67469070, ss71180732, ss75376733, ss119397739, ss160369949, ss172570295 NT_011109.16:24353053:C:T NC_000019.10:51581582:C: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 rs1543922

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.post596+ae089ad