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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.

rs5951434

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chrX:22297305 (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>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.374616 (99157/264690, TOPMED)
T=0.377227 (38940/103227, GnomAD)
T=0.48373 (10750/22223, 14KJPN) (+ 13 more)
T=0.38877 (7200/18520, ALFA)
T=0.48575 (6238/12842, 8.3KJPN)
T=0.4139 (1989/4805, 1000G_30x)
T=0.4215 (1591/3775, 1000G)
T=0.3838 (1423/3708, TWINSUK)
T=0.4942 (1446/2926, KOREAN)
T=0.3662 (1058/2889, ALSPAC)
T=0.427 (128/300, HapMap)
A=0.154 (43/280, SGDP_PRJ)
T=0.481 (52/108, Qatari)
T=0.42 (20/48, Vietnamese)
T=0.38 (15/40, GENOME_DK)
A=0.08 (2/26, 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 A=0.61123 T=0.38877
European Sub 14152 A=0.60719 T=0.39281
African Sub 2898 A=0.6246 T=0.3754
African Others Sub 114 A=0.605 T=0.395
African American Sub 2784 A=0.6254 T=0.3746
Asian Sub 112 A=0.562 T=0.438
East Asian Sub 86 A=0.60 T=0.40
Other Asian Sub 26 A=0.42 T=0.58
Latin American 1 Sub 146 A=0.644 T=0.356
Latin American 2 Sub 610 A=0.677 T=0.323
South Asian Sub 98 A=0.45 T=0.55
Other Sub 504 A=0.601 T=0.399


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=0.625384 T=0.374616
gnomAD - Genomes Global Study-wide 103227 A=0.622773 T=0.377227
gnomAD - Genomes European Sub 56688 A=0.60999 T=0.39001
gnomAD - Genomes African Sub 31027 A=0.63045 T=0.36955
gnomAD - Genomes American Sub 9257 A=0.6919 T=0.3081
gnomAD - Genomes Ashkenazi Jewish Sub 2507 A=0.6282 T=0.3718
gnomAD - Genomes East Asian Sub 2190 A=0.5374 T=0.4626
gnomAD - Genomes Other Sub 1558 A=0.6354 T=0.3646
14KJPN JAPANESE Study-wide 22223 A=0.51627 T=0.48373
Allele Frequency Aggregator Total Global 18520 A=0.61123 T=0.38877
Allele Frequency Aggregator European Sub 14152 A=0.60719 T=0.39281
Allele Frequency Aggregator African Sub 2898 A=0.6246 T=0.3754
Allele Frequency Aggregator Latin American 2 Sub 610 A=0.677 T=0.323
Allele Frequency Aggregator Other Sub 504 A=0.601 T=0.399
Allele Frequency Aggregator Latin American 1 Sub 146 A=0.644 T=0.356
Allele Frequency Aggregator Asian Sub 112 A=0.562 T=0.438
Allele Frequency Aggregator South Asian Sub 98 A=0.45 T=0.55
8.3KJPN JAPANESE Study-wide 12842 A=0.51425 T=0.48575
1000Genomes_30x Global Study-wide 4805 A=0.5861 T=0.4139
1000Genomes_30x African Sub 1328 A=0.6212 T=0.3788
1000Genomes_30x Europe Sub 961 A=0.614 T=0.386
1000Genomes_30x South Asian Sub 883 A=0.444 T=0.556
1000Genomes_30x East Asian Sub 878 A=0.539 T=0.461
1000Genomes_30x American Sub 755 A=0.710 T=0.290
1000Genomes Global Study-wide 3775 A=0.5785 T=0.4215
1000Genomes African Sub 1003 A=0.6072 T=0.3928
1000Genomes Europe Sub 766 A=0.619 T=0.381
1000Genomes East Asian Sub 764 A=0.538 T=0.462
1000Genomes South Asian Sub 718 A=0.451 T=0.549
1000Genomes American Sub 524 A=0.698 T=0.302
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.6162 T=0.3838
KOREAN population from KRGDB KOREAN Study-wide 2926 A=0.5058 T=0.4942
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 2889 A=0.6338 T=0.3662
HapMap Global Study-wide 300 A=0.573 T=0.427
HapMap American Sub 114 A=0.518 T=0.482
HapMap African Sub 108 A=0.667 T=0.333
HapMap Asian Sub 78 A=0.53 T=0.47
SGDP_PRJ Global Study-wide 280 A=0.154 T=0.846
Qatari Global Study-wide 108 A=0.519 T=0.481
A Vietnamese Genetic Variation Database Global Study-wide 48 A=0.58 T=0.42
The Danish reference pan genome Danish Study-wide 40 A=0.62 T=0.38
Siberian Global Study-wide 26 A=0.08 T=0.92
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.22297305A>T
GRCh37.p13 chr X NC_000023.10:g.22315422A>T
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 A= T
GRCh38.p14 chr X NC_000023.11:g.22297305= NC_000023.11:g.22297305A>T
GRCh37.p13 chr X NC_000023.10:g.22315422= NC_000023.10:g.22315422A>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#.

61 SubSNP, 16 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_SNP ss8236455 Apr 21, 2003 (114)
2 WI_SSAHASNP ss12056871 Jul 11, 2003 (117)
3 SC_SNP ss15865894 Feb 27, 2004 (120)
4 CSHL-HAPMAP ss18051808 Feb 27, 2004 (120)
5 PERLEGEN ss24230573 Sep 20, 2004 (123)
6 ABI ss43562011 Mar 14, 2006 (126)
7 PERLEGEN ss69258830 May 17, 2007 (127)
8 HGSV ss78716927 Dec 06, 2007 (129)
9 HGSV ss84739788 Dec 15, 2007 (130)
10 1000GENOMES ss112808472 Jan 25, 2009 (130)
11 1000GENOMES ss114508283 Jan 25, 2009 (130)
12 ILLUMINA-UK ss115597712 Feb 06, 2009 (130)
13 ENSEMBL ss161781855 Dec 01, 2009 (131)
14 COMPLETE_GENOMICS ss163054872 Jul 04, 2010 (132)
15 COMPLETE_GENOMICS ss164561014 Jul 04, 2010 (132)
16 BCM-HGSC-SUB ss208861443 Jul 04, 2010 (132)
17 GMI ss283708498 May 04, 2012 (137)
18 PJP ss294532299 May 09, 2011 (134)
19 1000GENOMES ss341355629 May 09, 2011 (134)
20 TISHKOFF ss566793429 Apr 25, 2013 (138)
21 SSMP ss662725385 Apr 25, 2013 (138)
22 JMKIDD_LAB ss1082825353 Aug 21, 2014 (142)
23 DDI ss1432013015 Apr 01, 2015 (144)
24 1000GENOMES ss1553766713 Apr 01, 2015 (144)
25 EVA_GENOME_DK ss1583344022 Apr 01, 2015 (144)
26 EVA_UK10K_ALSPAC ss1640453580 Apr 01, 2015 (144)
27 EVA_UK10K_TWINSUK ss1683447613 Apr 01, 2015 (144)
28 WEILL_CORNELL_DGM ss1939198778 Feb 12, 2016 (147)
29 ILLUMINA ss1958181215 Feb 12, 2016 (147)
30 GENOMED ss1971351524 Jul 19, 2016 (147)
31 USC_VALOUEV ss2158976397 Dec 20, 2016 (150)
32 HUMAN_LONGEVITY ss2316156654 Dec 20, 2016 (150)
33 SYSTEMSBIOZJU ss2629674459 Nov 08, 2017 (151)
34 ILLUMINA ss2635201476 Nov 08, 2017 (151)
35 GRF ss2710103543 Nov 08, 2017 (151)
36 GNOMAD ss2977138000 Nov 08, 2017 (151)
37 SWEGEN ss3019722199 Nov 08, 2017 (151)
38 ILLUMINA ss3022994731 Nov 08, 2017 (151)
39 BIOINF_KMB_FNS_UNIBA ss3029016734 Nov 08, 2017 (151)
40 ILLUMINA ss3653553144 Oct 12, 2018 (152)
41 ILLUMINA ss3726667233 Jul 13, 2019 (153)
42 EVA ss3769985002 Jul 13, 2019 (153)
43 KHV_HUMAN_GENOMES ss3822828146 Jul 13, 2019 (153)
44 EVA ss3836112403 Apr 27, 2020 (154)
45 EVA ss3841672272 Apr 27, 2020 (154)
46 EVA ss3847189523 Apr 27, 2020 (154)
47 SGDP_PRJ ss3891116873 Apr 27, 2020 (154)
48 KRGDB ss3941475878 Apr 27, 2020 (154)
49 TOPMED ss5117528538 Apr 26, 2021 (155)
50 TOMMO_GENOMICS ss5233795350 Apr 26, 2021 (155)
51 EVA ss5237621777 Apr 26, 2021 (155)
52 1000G_HIGH_COVERAGE ss5312007012 Oct 16, 2022 (156)
53 HUGCELL_USP ss5503732594 Oct 16, 2022 (156)
54 1000G_HIGH_COVERAGE ss5619945085 Oct 16, 2022 (156)
55 SANFORD_IMAGENETICS ss5664970023 Oct 16, 2022 (156)
56 TOMMO_GENOMICS ss5795302241 Oct 16, 2022 (156)
57 YY_MCH ss5818928756 Oct 16, 2022 (156)
58 EVA ss5848229121 Oct 16, 2022 (156)
59 EVA ss5857031224 Oct 16, 2022 (156)
60 EVA ss5977941530 Oct 16, 2022 (156)
61 EVA ss5979913044 Oct 16, 2022 (156)
62 1000Genomes NC_000023.10 - 22315422 Oct 12, 2018 (152)
63 1000Genomes_30x NC_000023.11 - 22297305 Oct 16, 2022 (156)
64 The Avon Longitudinal Study of Parents and Children NC_000023.10 - 22315422 Oct 12, 2018 (152)
65 The Danish reference pan genome NC_000023.10 - 22315422 Apr 27, 2020 (154)
66 gnomAD - Genomes NC_000023.11 - 22297305 Apr 26, 2021 (155)
67 HapMap NC_000023.11 - 22297305 Apr 27, 2020 (154)
68 KOREAN population from KRGDB NC_000023.10 - 22315422 Apr 27, 2020 (154)
69 Qatari NC_000023.10 - 22315422 Apr 27, 2020 (154)
70 SGDP_PRJ NC_000023.10 - 22315422 Apr 27, 2020 (154)
71 Siberian NC_000023.10 - 22315422 Apr 27, 2020 (154)
72 8.3KJPN NC_000023.10 - 22315422 Apr 26, 2021 (155)
73 14KJPN NC_000023.11 - 22297305 Oct 16, 2022 (156)
74 TopMed NC_000023.11 - 22297305 Apr 26, 2021 (155)
75 UK 10K study - Twins NC_000023.10 - 22315422 Oct 12, 2018 (152)
76 A Vietnamese Genetic Variation Database NC_000023.10 - 22315422 Jul 13, 2019 (153)
77 ALFA NC_000023.11 - 22297305 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)
rs7892255 Aug 26, 2003 (117)
rs17275509 Oct 07, 2004 (123)
rs60918519 May 26, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss78716927, ss84739788 NC_000023.8:22075078:A:T NC_000023.11:22297304:A:T (self)
ss112808472, ss114508283, ss115597712, ss163054872, ss164561014, ss208861443, ss283708498, ss294532299, ss2635201476 NC_000023.9:22225342:A:T NC_000023.11:22297304:A:T (self)
81748277, 45154720, 9508959, 48653272, 21240700, 43133853, 11492751, 91764657, 45154720, 9958947, ss341355629, ss566793429, ss662725385, ss1082825353, ss1432013015, ss1553766713, ss1583344022, ss1640453580, ss1683447613, ss1939198778, ss1958181215, ss1971351524, ss2158976397, ss2629674459, ss2710103543, ss2977138000, ss3019722199, ss3022994731, ss3653553144, ss3769985002, ss3836112403, ss3841672272, ss3891116873, ss3941475878, ss5233795350, ss5237621777, ss5664970023, ss5848229121, ss5977941530, ss5979913044 NC_000023.10:22315421:A:T NC_000023.11:22297304:A:T (self)
107471020, 576725591, 3957219, 129139345, 681134895, 13429054740, ss2316156654, ss3029016734, ss3726667233, ss3822828146, ss3847189523, ss5117528538, ss5312007012, ss5503732594, ss5619945085, ss5795302241, ss5818928756, ss5857031224 NC_000023.11:22297304:A:T NC_000023.11:22297304:A:T (self)
ss12056871 NT_011757.12:9229888:A:T NC_000023.11:22297304:A:T (self)
ss15865894, ss18051808 NT_011757.13:18281986:A:T NC_000023.11:22297304:A:T (self)
ss8236455, ss24230573, ss43562011, ss69258830, ss161781855 NT_167197.1:20197183:A:T NC_000023.11:22297304: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 rs5951434

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