Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation

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.

rs5951417

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chrX:22268894 (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=0.062590 (16567/264690, TOPMED)
A=0.052847 (5493/103941, GnomAD)
A=0.26900 (5978/22223, 14KJPN) (+ 12 more)
A=0.02743 (508/18520, ALFA)
A=0.26497 (3403/12843, 8.3KJPN)
A=0.0993 (477/4805, 1000G_30x)
A=0.1012 (382/3775, 1000G)
A=0.0008 (3/3708, TWINSUK)
A=0.2358 (691/2930, KOREAN)
A=0.0003 (1/2889, ALSPAC)
A=0.105 (20/190, HapMap)
A=0.046 (5/108, Qatari)
G=0.19 (14/74, SGDP_PRJ)
A=0.26 (12/47, Vietnamese)
G=0.2 (1/4, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
PTCHD1-AS : 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 18520 G=0.97257 A=0.02743
European Sub 14152 G=0.99809 A=0.00191
African Sub 2898 G=0.8744 A=0.1256
African Others Sub 114 G=0.921 A=0.079
African American Sub 2784 G=0.8725 A=0.1275
Asian Sub 112 G=0.696 A=0.304
East Asian Sub 86 G=0.70 A=0.30
Other Asian Sub 26 G=0.69 A=0.31
Latin American 1 Sub 146 G=0.932 A=0.068
Latin American 2 Sub 610 G=0.938 A=0.062
South Asian Sub 98 G=1.00 A=0.00
Other Sub 504 G=0.931 A=0.069


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=0.937410 A=0.062590
gnomAD - Genomes Global Study-wide 103941 G=0.947153 A=0.052847
gnomAD - Genomes European Sub 57140 G=0.99835 A=0.00165
gnomAD - Genomes African Sub 31190 G=0.86973 A=0.13027
gnomAD - Genomes American Sub 9305 G=0.9293 A=0.0707
gnomAD - Genomes Ashkenazi Jewish Sub 2536 G=0.9941 A=0.0059
gnomAD - Genomes East Asian Sub 2211 G=0.7417 A=0.2583
gnomAD - Genomes Other Sub 1559 G=0.9410 A=0.0590
14KJPN JAPANESE Study-wide 22223 G=0.73100 A=0.26900
Allele Frequency Aggregator Total Global 18520 G=0.97257 A=0.02743
Allele Frequency Aggregator European Sub 14152 G=0.99809 A=0.00191
Allele Frequency Aggregator African Sub 2898 G=0.8744 A=0.1256
Allele Frequency Aggregator Latin American 2 Sub 610 G=0.938 A=0.062
Allele Frequency Aggregator Other Sub 504 G=0.931 A=0.069
Allele Frequency Aggregator Latin American 1 Sub 146 G=0.932 A=0.068
Allele Frequency Aggregator Asian Sub 112 G=0.696 A=0.304
Allele Frequency Aggregator South Asian Sub 98 G=1.00 A=0.00
8.3KJPN JAPANESE Study-wide 12843 G=0.73503 A=0.26497
1000Genomes_30x Global Study-wide 4805 G=0.9007 A=0.0993
1000Genomes_30x African Sub 1328 G=0.8456 A=0.1544
1000Genomes_30x Europe Sub 961 G=0.998 A=0.002
1000Genomes_30x South Asian Sub 883 G=0.985 A=0.015
1000Genomes_30x East Asian Sub 878 G=0.767 A=0.233
1000Genomes_30x American Sub 755 G=0.931 A=0.069
1000Genomes Global Study-wide 3775 G=0.8988 A=0.1012
1000Genomes African Sub 1003 G=0.8495 A=0.1505
1000Genomes Europe Sub 766 G=0.997 A=0.003
1000Genomes East Asian Sub 764 G=0.767 A=0.233
1000Genomes South Asian Sub 718 G=0.985 A=0.015
1000Genomes American Sub 524 G=0.924 A=0.076
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.9992 A=0.0008
KOREAN population from KRGDB KOREAN Study-wide 2930 G=0.7642 A=0.2358
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 2889 G=0.9997 A=0.0003
HapMap Global Study-wide 190 G=0.895 A=0.105
HapMap American Sub 104 G=1.000 A=0.000
HapMap Asian Sub 86 G=0.77 A=0.23
Qatari Global Study-wide 108 G=0.954 A=0.046
SGDP_PRJ Global Study-wide 74 G=0.19 A=0.81
A Vietnamese Genetic Variation Database Global Study-wide 47 G=0.74 A=0.26
Siberian 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.22268894G>A
GRCh37.p13 chr X NC_000023.10:g.22287011G>A
CBLL2 RefSeqGene NG_021438.1:g.952G>A
Gene: PTCHD1-AS, PTCHD1 antisense RNA (head to head) (minus strand)
Molecule type Change Amino acid[Codon] SO Term
PTCHD1-AS transcript NR_073010.2:n. 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 G= A
GRCh38.p14 chr X NC_000023.11:g.22268894= NC_000023.11:g.22268894G>A
GRCh37.p13 chr X NC_000023.10:g.22287011= NC_000023.10:g.22287011G>A
CBLL2 RefSeqGene NG_021438.1:g.952= NG_021438.1:g.952G>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#.

34 SubSNP, 15 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_SNP ss8236436 Apr 21, 2003 (114)
2 HGSV ss82223982 Dec 15, 2007 (130)
3 GMI ss283708422 May 04, 2012 (137)
4 PJP ss294532260 May 09, 2011 (134)
5 1000GENOMES ss341355419 May 09, 2011 (134)
6 TISHKOFF ss566793296 Apr 25, 2013 (138)
7 SSMP ss662725274 Apr 25, 2013 (138)
8 JMKIDD_LAB ss1082825206 Aug 21, 2014 (142)
9 1000GENOMES ss1553765930 Apr 01, 2015 (144)
10 EVA_UK10K_ALSPAC ss1640453231 Apr 01, 2015 (144)
11 EVA_UK10K_TWINSUK ss1683447264 Apr 01, 2015 (144)
12 WEILL_CORNELL_DGM ss1939198590 Feb 12, 2016 (147)
13 USC_VALOUEV ss2158976294 Dec 20, 2016 (150)
14 HUMAN_LONGEVITY ss2316155272 Dec 20, 2016 (150)
15 SYSTEMSBIOZJU ss2629674405 Nov 08, 2017 (151)
16 ILLUMINA ss2634944620 Nov 08, 2017 (151)
17 GRF ss2710103435 Nov 08, 2017 (151)
18 GNOMAD ss2977136218 Nov 08, 2017 (151)
19 SWEGEN ss3019721954 Nov 08, 2017 (151)
20 EVA ss3769984762 Jul 13, 2019 (153)
21 KHV_HUMAN_GENOMES ss3822827916 Jul 13, 2019 (153)
22 EVA ss3836112313 Apr 27, 2020 (154)
23 SGDP_PRJ ss3891116502 Apr 27, 2020 (154)
24 KRGDB ss3941475476 Apr 27, 2020 (154)
25 TOPMED ss5117523118 Apr 26, 2021 (155)
26 TOMMO_GENOMICS ss5233794611 Apr 26, 2021 (155)
27 1000G_HIGH_COVERAGE ss5312006391 Oct 16, 2022 (156)
28 HUGCELL_USP ss5503731999 Oct 16, 2022 (156)
29 1000G_HIGH_COVERAGE ss5619944160 Oct 16, 2022 (156)
30 SANFORD_IMAGENETICS ss5664969680 Oct 16, 2022 (156)
31 TOMMO_GENOMICS ss5795301304 Oct 16, 2022 (156)
32 YY_MCH ss5818928590 Oct 16, 2022 (156)
33 EVA ss5857031138 Oct 16, 2022 (156)
34 EVA ss5977941136 Oct 16, 2022 (156)
35 1000Genomes NC_000023.10 - 22287011 Oct 12, 2018 (152)
36 1000Genomes_30x NC_000023.11 - 22268894 Oct 16, 2022 (156)
37 The Avon Longitudinal Study of Parents and Children NC_000023.10 - 22287011 Oct 12, 2018 (152)
38 gnomAD - Genomes NC_000023.11 - 22268894 Apr 26, 2021 (155)
39 HapMap NC_000023.11 - 22268894 Apr 27, 2020 (154)
40 KOREAN population from KRGDB NC_000023.10 - 22287011 Apr 27, 2020 (154)
41 Qatari NC_000023.10 - 22287011 Apr 27, 2020 (154)
42 SGDP_PRJ NC_000023.10 - 22287011 Apr 27, 2020 (154)
43 Siberian NC_000023.10 - 22287011 Apr 27, 2020 (154)
44 8.3KJPN NC_000023.10 - 22287011 Apr 26, 2021 (155)
45 14KJPN NC_000023.11 - 22268894 Oct 16, 2022 (156)
46 TopMed NC_000023.11 - 22268894 Apr 26, 2021 (155)
47 UK 10K study - Twins NC_000023.10 - 22287011 Oct 12, 2018 (152)
48 A Vietnamese Genetic Variation Database NC_000023.10 - 22287011 Jul 13, 2019 (153)
49 ALFA NC_000023.11 - 22268894 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).

Associated ID History Updated (Build)
rs60753107 May 26, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss82223982 NC_000023.8:22046667:G:A NC_000023.11:22268893:G:A (self)
ss283708422, ss294532260 NC_000023.9:22196931:G:A NC_000023.11:22268893:G:A (self)
81747500, 45154351, 48652870, 21240512, 43133482, 11492648, 91763918, 45154351, 9958846, ss341355419, ss566793296, ss662725274, ss1082825206, ss1553765930, ss1640453231, ss1683447264, ss1939198590, ss2158976294, ss2629674405, ss2634944620, ss2710103435, ss2977136218, ss3019721954, ss3769984762, ss3836112313, ss3891116502, ss3941475476, ss5233794611, ss5664969680, ss5977941136 NC_000023.10:22287010:G:A NC_000023.11:22268893:G:A (self)
107470095, 576721392, 3957151, 129138408, 681129475, 2123630283, ss2316155272, ss3822827916, ss5117523118, ss5312006391, ss5503731999, ss5619944160, ss5795301304, ss5818928590, ss5857031138 NC_000023.11:22268893:G:A NC_000023.11:22268893:G:A (self)
ss8236436 NT_167197.1:20168772:G:A NC_000023.11:22268893: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 rs5951417

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