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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.

rs189924262

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chrX:41474651 (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
G>A
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.001439 (381/264690, TOPMED)
A=0.002428 (376/154889, GnomAD_exome)
A=0.000887 (92/103682, GnomAD) (+ 10 more)
A=0.00127 (117/92010, ALFA)
A=0.00326 (136/41728, ExAC)
A=0.00140 (31/22212, 14KJPN)
A=0.00148 (19/12832, 8.3KJPN)
A=0.00019 (2/10539, GO-ESP)
A=0.0060 (29/4805, 1000G_30x)
A=0.0061 (23/3775, 1000G)
A=0.0072 (21/2914, KOREAN)
A=0.047 (7/148, Vietnamese)
G=0.2 (1/4, SGDP_PRJ)
Clinical Significance
Reported in ClinVar
Gene : Consequence
NYX : Missense 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 92010 G=0.99873 A=0.00127
European Sub 74088 G=0.99993 A=0.00007
African Sub 3620 G=0.9994 A=0.0006
African Others Sub 124 G=1.000 A=0.000
African American Sub 3496 G=0.9994 A=0.0006
Asian Sub 3124 G=0.9789 A=0.0211
East Asian Sub 1894 G=0.9768 A=0.0232
Other Asian Sub 1230 G=0.9821 A=0.0179
Latin American 1 Sub 146 G=1.000 A=0.000
Latin American 2 Sub 630 G=1.000 A=0.000
South Asian Sub 98 G=1.00 A=0.00
Other Sub 10304 G=0.99573 A=0.00427


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 G=0.998561 A=0.001439
gnomAD - Exomes Global Study-wide 154889 G=0.997572 A=0.002428
gnomAD - Exomes European Sub 79823 G=0.99999 A=0.00001
gnomAD - Exomes Asian Sub 28557 G=0.98722 A=0.01278
gnomAD - Exomes American Sub 24854 G=1.00000 A=0.00000
gnomAD - Exomes African Sub 10941 G=0.99936 A=0.00064
gnomAD - Exomes Ashkenazi Jewish Sub 6789 G=1.0000 A=0.0000
gnomAD - Exomes Other Sub 3925 G=0.9992 A=0.0008
gnomAD - Genomes Global Study-wide 103682 G=0.999113 A=0.000887
gnomAD - Genomes European Sub 56918 G=1.00000 A=0.00000
gnomAD - Genomes African Sub 31175 G=0.99958 A=0.00042
gnomAD - Genomes American Sub 9311 G=0.9998 A=0.0002
gnomAD - Genomes Ashkenazi Jewish Sub 2521 G=1.0000 A=0.0000
gnomAD - Genomes East Asian Sub 2199 G=0.9654 A=0.0346
gnomAD - Genomes Other Sub 1558 G=0.9994 A=0.0006
Allele Frequency Aggregator Total Global 92010 G=0.99873 A=0.00127
Allele Frequency Aggregator European Sub 74088 G=0.99993 A=0.00007
Allele Frequency Aggregator Other Sub 10304 G=0.99573 A=0.00427
Allele Frequency Aggregator African Sub 3620 G=0.9994 A=0.0006
Allele Frequency Aggregator Asian Sub 3124 G=0.9789 A=0.0211
Allele Frequency Aggregator Latin American 2 Sub 630 G=1.000 A=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 G=1.000 A=0.000
Allele Frequency Aggregator South Asian Sub 98 G=1.00 A=0.00
ExAC Global Study-wide 41728 G=0.99674 A=0.00326
ExAC Europe Sub 23087 G=1.00000 A=0.00000
ExAC Asian Sub 9821 G=0.9870 A=0.0130
ExAC African Sub 4761 G=0.9985 A=0.0015
ExAC American Sub 3784 G=1.0000 A=0.0000
ExAC Other Sub 275 G=0.996 A=0.004
14KJPN JAPANESE Study-wide 22212 G=0.99860 A=0.00140
8.3KJPN JAPANESE Study-wide 12832 G=0.99852 A=0.00148
GO Exome Sequencing Project Global Study-wide 10539 G=0.99981 A=0.00019
GO Exome Sequencing Project European American Sub 6709 G=1.0000 A=0.0000
GO Exome Sequencing Project African American Sub 3830 G=0.9995 A=0.0005
1000Genomes_30x Global Study-wide 4805 G=0.9940 A=0.0060
1000Genomes_30x African Sub 1328 G=1.0000 A=0.0000
1000Genomes_30x Europe Sub 961 G=1.000 A=0.000
1000Genomes_30x South Asian Sub 883 G=1.000 A=0.000
1000Genomes_30x East Asian Sub 878 G=0.967 A=0.033
1000Genomes_30x American Sub 755 G=1.000 A=0.000
1000Genomes Global Study-wide 3775 G=0.9939 A=0.0061
1000Genomes African Sub 1003 G=1.0000 A=0.0000
1000Genomes Europe Sub 766 G=1.000 A=0.000
1000Genomes East Asian Sub 764 G=0.970 A=0.030
1000Genomes South Asian Sub 718 G=1.000 A=0.000
1000Genomes American Sub 524 G=1.000 A=0.000
KOREAN population from KRGDB KOREAN Study-wide 2914 G=0.9928 A=0.0072
A Vietnamese Genetic Variation Database Global Study-wide 148 G=0.953 A=0.047
SGDP_PRJ Global Study-wide 4 G=0.2 A=0.8
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 X NC_000023.11:g.41474651G>A
GRCh37.p13 chr X NC_000023.10:g.41333904G>A
NYX RefSeqGene NG_009112.1:g.32192G>A
Gene: NYX, nyctalopin (plus strand)
Molecule type Change Amino acid[Codon] SO Term
NYX transcript variant 2 NM_001378477.3:c.1183G>A G [GGC] > S [AGC] Coding Sequence Variant
nyctalopin precursor NP_001365406.2:p.Gly395Ser G (Gly) > S (Ser) Missense Variant
NYX transcript variant 1 NM_022567.3:c.1183G>A G [GGC] > S [AGC] Coding Sequence Variant
nyctalopin precursor NP_072089.2:p.Gly395Ser G (Gly) > S (Ser) 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: A (allele ID: 348731 )
ClinVar Accession Disease Names Clinical Significance
RCV000266696.3 Congenital stationary night blindness 1A Likely-Benign
RCV001520041.4 not provided Benign
RCV001699409.3 not specified 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 G= A
GRCh38.p14 chr X NC_000023.11:g.41474651= NC_000023.11:g.41474651G>A
GRCh37.p13 chr X NC_000023.10:g.41333904= NC_000023.10:g.41333904G>A
NYX RefSeqGene NG_009112.1:g.32192= NG_009112.1:g.32192G>A
NYX transcript variant 1 NM_022567.3:c.1183= NM_022567.3:c.1183G>A
NYX transcript variant 1 NM_022567.2:c.1198= NM_022567.2:c.1198G>A
NYX transcript variant 2 NM_001378477.3:c.1183= NM_001378477.3:c.1183G>A
NYX transcript variant 2 NM_001378477.2:c.1198= NM_001378477.2:c.1198G>A
NYX transcript variant 2 NM_001378477.1:c.1198= NM_001378477.1:c.1198G>A
nyctalopin precursor NP_072089.2:p.Gly395= NP_072089.2:p.Gly395Ser
nyctalopin precursor NP_001365406.2:p.Gly395= NP_001365406.2:p.Gly395Ser
nyctalopin precursor NP_072089.1:p.Gly400= NP_072089.1:p.Gly400Ser
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#.

44 SubSNP, 13 Frequency, 3 ClinVar submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss466466067 Sep 17, 2011 (135)
2 ILLUMINA ss482829128 May 04, 2012 (137)
3 ILLUMINA ss484375453 May 04, 2012 (137)
4 1000GENOMES ss491199720 May 04, 2012 (137)
5 EXOME_CHIP ss491576185 May 04, 2012 (137)
6 NHLBI-ESP ss713648577 Apr 25, 2013 (138)
7 ILLUMINA ss781891435 Sep 08, 2015 (146)
8 ILLUMINA ss783466937 Sep 08, 2015 (146)
9 1000GENOMES ss1554202773 Apr 01, 2015 (144)
10 EVA_EXAC ss1694496207 Apr 01, 2015 (144)
11 ILLUMINA ss1752806716 Sep 08, 2015 (146)
12 ILLUMINA ss1917716997 Feb 12, 2016 (147)
13 ILLUMINA ss1945972146 Feb 12, 2016 (147)
14 ILLUMINA ss1958189901 Feb 12, 2016 (147)
15 HUMAN_LONGEVITY ss2316962036 Dec 20, 2016 (150)
16 GNOMAD ss2745365937 Nov 08, 2017 (151)
17 GNOMAD ss2746094418 Nov 08, 2017 (151)
18 GNOMAD ss2978215103 Nov 08, 2017 (151)
19 AFFY ss2985483895 Nov 08, 2017 (151)
20 ILLUMINA ss3023003738 Nov 08, 2017 (151)
21 ILLUMINA ss3635247568 Oct 12, 2018 (152)
22 ILLUMINA ss3640955050 Oct 12, 2018 (152)
23 ILLUMINA ss3645011186 Oct 12, 2018 (152)
24 ILLUMINA ss3653562218 Oct 12, 2018 (152)
25 ILLUMINA ss3654250460 Oct 12, 2018 (152)
26 ILLUMINA ss3744598356 Jul 13, 2019 (153)
27 ILLUMINA ss3745547986 Jul 13, 2019 (153)
28 EVA ss3770104256 Jul 13, 2019 (153)
29 ILLUMINA ss3773039689 Jul 13, 2019 (153)
30 KHV_HUMAN_GENOMES ss3822938332 Jul 13, 2019 (153)
31 EVA ss3825481110 Apr 27, 2020 (154)
32 SGDP_PRJ ss3891323121 Apr 27, 2020 (154)
33 KRGDB ss3941719821 Apr 27, 2020 (154)
34 EVA ss3984765266 Apr 27, 2021 (155)
35 TOPMED ss5120965396 Apr 27, 2021 (155)
36 TOMMO_GENOMICS ss5234221378 Apr 27, 2021 (155)
37 EVA ss5237055996 Apr 27, 2021 (155)
38 1000G_HIGH_COVERAGE ss5312356898 Oct 16, 2022 (156)
39 TRAN_CS_UWATERLOO ss5314459205 Oct 16, 2022 (156)
40 1000G_HIGH_COVERAGE ss5620490317 Oct 16, 2022 (156)
41 TOMMO_GENOMICS ss5795854103 Oct 16, 2022 (156)
42 YY_MCH ss5819006510 Oct 16, 2022 (156)
43 EVA ss5848231550 Oct 16, 2022 (156)
44 EVA ss5978141486 Oct 16, 2022 (156)
45 1000Genomes NC_000023.10 - 41333904 Oct 12, 2018 (152)
46 1000Genomes_30x NC_000023.11 - 41474651 Oct 16, 2022 (156)
47 ExAC NC_000023.10 - 41333904 Oct 12, 2018 (152)
48 gnomAD - Genomes NC_000023.11 - 41474651 Apr 27, 2021 (155)
49 gnomAD - Exomes NC_000023.10 - 41333904 Jul 13, 2019 (153)
50 GO Exome Sequencing Project NC_000023.10 - 41333904 Oct 12, 2018 (152)
51 KOREAN population from KRGDB NC_000023.10 - 41333904 Apr 27, 2020 (154)
52 SGDP_PRJ NC_000023.10 - 41333904 Apr 27, 2020 (154)
53 8.3KJPN NC_000023.10 - 41333904 Apr 27, 2021 (155)
54 14KJPN NC_000023.11 - 41474651 Oct 16, 2022 (156)
55 TopMed NC_000023.11 - 41474651 Apr 27, 2021 (155)
56 A Vietnamese Genetic Variation Database NC_000023.10 - 41333904 Jul 13, 2019 (153)
57 ALFA NC_000023.11 - 41474651 Apr 27, 2021 (155)
58 ClinVar RCV000266696.3 Oct 16, 2022 (156)
59 ClinVar RCV001520041.4 Oct 16, 2022 (156)
60 ClinVar RCV001699409.3 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).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss484375453 NC_000023.9:41218847:G:A NC_000023.11:41474650:G:A (self)
82179888, 9996400, 14701927, 1937903, 48897215, 43340101, 92190685, 10004011, ss466466067, ss482829128, ss491199720, ss491576185, ss713648577, ss781891435, ss783466937, ss1554202773, ss1694496207, ss1752806716, ss1917716997, ss1945972146, ss1958189901, ss2745365937, ss2746094418, ss2978215103, ss2985483895, ss3023003738, ss3635247568, ss3640955050, ss3645011186, ss3653562218, ss3654250460, ss3744598356, ss3745547986, ss3770104256, ss3773039689, ss3825481110, ss3891323121, ss3941719821, ss3984765266, ss5234221378, ss5848231550, ss5978141486 NC_000023.10:41333903:G:A NC_000023.11:41474650:G:A (self)
RCV000266696.3, RCV001520041.4, RCV001699409.3, 108016252, 579286737, 129691207, 684571753, 978865457, ss2316962036, ss3822938332, ss5120965396, ss5237055996, ss5312356898, ss5314459205, ss5620490317, ss5795854103, ss5819006510 NC_000023.11:41474650:G:A NC_000023.11:41474650:G:A (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 rs189924262

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