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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.

rs61158452

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:63736-63741 (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
delCTA
Variation Type
Indel Insertion and Deletion
Frequency
delCTA=0.288397 (29026/100646, GnomAD)
(CTA)2=0.37207 (6134/16486, 8.3KJPN)
delCTA=0.22967 (3706/16136, ALFA) (+ 5 more)
delCTA=0.3718 (1862/5008, 1000G)
(CTA)2=0.3217 (579/1800, Korea1K)
delCTA=0.301 (300/998, GoNL)
delCTA=0.267 (153/572, NorthernSweden)
delCTA=0.24 (9/38, GENOME_DK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
OR4F5 : 2KB Upstream 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 1 NC_000001.11:g.63736CTA[1]
GRCh37.p13 chr 1 NC_000001.10:g.63736CTA[1]
OR4G11P pseudogene NG_004423.3:g.821CTA[1]
Gene: OR4F5, olfactory receptor family 4 subfamily F member 5 (plus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
OR4F5 transcript NM_001005484.2:c. N/A Upstream Transcript 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 16136 CTACTA=0.77033 CTA=0.22967
European Sub 11886 CTACTA=0.75576 CTA=0.24424
African Sub 2816 CTACTA=0.8615 CTA=0.1385
African Others Sub 108 CTACTA=0.898 CTA=0.102
African American Sub 2708 CTACTA=0.8600 CTA=0.1400
Asian Sub 108 CTACTA=0.269 CTA=0.731
East Asian Sub 84 CTACTA=0.25 CTA=0.75
Other Asian Sub 24 CTACTA=0.33 CTA=0.67
Latin American 1 Sub 146 CTACTA=0.788 CTA=0.212
Latin American 2 Sub 610 CTACTA=0.744 CTA=0.256
South Asian Sub 94 CTACTA=0.53 CTA=0.47
Other Sub 476 CTACTA=0.784 CTA=0.216


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
gnomAD - Genomes Global Study-wide 100646 (CTA)2=0.711603 delCTA=0.288397
gnomAD - Genomes European Sub 50044 (CTA)2=0.65640 delCTA=0.34360
gnomAD - Genomes African Sub 35098 (CTA)2=0.83734 delCTA=0.16266
gnomAD - Genomes American Sub 9114 (CTA)2=0.6648 delCTA=0.3352
gnomAD - Genomes East Asian Sub 2884 (CTA)2=0.3336 delCTA=0.6664
gnomAD - Genomes Ashkenazi Jewish Sub 2002 (CTA)2=0.6678 delCTA=0.3322
gnomAD - Genomes Other Sub 1504 (CTA)2=0.6809 delCTA=0.3191
8.3KJPN JAPANESE Study-wide 16486 (CTA)2=0.37207 delCTA=0.62793
1000Genomes Global Study-wide 5008 (CTA)2=0.6282 delCTA=0.3718
1000Genomes African Sub 1322 (CTA)2=0.8926 delCTA=0.1074
1000Genomes East Asian Sub 1008 (CTA)2=0.2708 delCTA=0.7292
1000Genomes Europe Sub 1006 (CTA)2=0.6610 delCTA=0.3390
1000Genomes South Asian Sub 978 (CTA)2=0.554 delCTA=0.446
1000Genomes American Sub 694 (CTA)2=0.700 delCTA=0.300
Korean Genome Project KOREAN Study-wide 1800 (CTA)2=0.3217 delCTA=0.6783
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 (CTA)2=0.699 delCTA=0.301
Northern Sweden ACPOP Study-wide 572 (CTA)2=0.733 delCTA=0.267
The Danish reference pan genome Danish Study-wide 38 (CTA)2=0.76 delCTA=0.24
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 (CTA)2= delCTA
GRCh38.p13 chr 1 NC_000001.11:g.63736_63741= NC_000001.11:g.63736CTA[1]
GRCh37.p13 chr 1 NC_000001.10:g.63736_63741= NC_000001.10:g.63736CTA[1]
OR4G11P pseudogene NG_004423.3:g.821_826= NG_004423.3:g.821CTA[1]
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#.

22 SubSNP, 8 Frequency submissions
No Submitter Submission ID Date (Build)
1 HGSV ss82065714 Dec 16, 2007 (129)
2 HGSV ss82180254 Dec 16, 2007 (129)
3 BGI ss104663000 Mar 15, 2016 (147)
4 GMI ss287939195 May 04, 2012 (137)
5 1000GENOMES ss498763760 May 04, 2012 (137)
6 LUNTER ss550899109 Apr 25, 2013 (138)
7 LUNTER ss550903083 Apr 25, 2013 (138)
8 LUNTER ss552738961 Apr 25, 2013 (138)
9 SSMP ss663198146 Apr 01, 2015 (144)
10 BILGI_BIOE ss666079955 Apr 25, 2013 (138)
11 EVA-GONL ss974768773 Aug 21, 2014 (142)
12 1000GENOMES ss1367645216 Aug 21, 2014 (142)
13 EVA_GENOME_DK ss1573867000 Apr 01, 2015 (144)
14 GNOMAD ss2750604475 Nov 08, 2017 (151)
15 SWEGEN ss2986142050 Nov 08, 2017 (151)
16 MCHAISSO ss3063573409 Nov 08, 2017 (151)
17 TOPMED ss3066322496 Nov 08, 2017 (151)
18 EVA_DECODE ss3685990409 Jul 12, 2019 (153)
19 ACPOP ss3726715213 Jul 12, 2019 (153)
20 KHV_HUMAN_GENOMES ss3798742489 Jul 12, 2019 (153)
21 KOGIC ss3943622692 Apr 25, 2020 (154)
22 TOMMO_GENOMICS ss5142033027 Apr 25, 2021 (155)
23 1000Genomes NC_000001.10 - 63736 Oct 11, 2018 (152)
24 The Danish reference pan genome NC_000001.10 - 63736 Apr 25, 2020 (154)
25 gnomAD - Genomes NC_000001.11 - 63736 Apr 25, 2021 (155)
26 Genome of the Netherlands Release 5 NC_000001.10 - 63736 Apr 25, 2020 (154)
27 Korean Genome Project NC_000001.11 - 63736 Apr 25, 2020 (154)
28 Northern Sweden NC_000001.10 - 63736 Jul 12, 2019 (153)
29 8.3KJPN NC_000001.10 - 63736 Apr 25, 2021 (155)
30 ALFA NC_000001.11 - 63736 Apr 25, 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
ss82065714, ss82180254 NC_000001.8:53601:CTA: NC_000001.11:63735:CTACTA:CTA (self)
ss287939195, ss550899109, ss550903083, ss552738961 NC_000001.9:53598:CTA: NC_000001.11:63735:CTACTA:CTA (self)
372, 120132, 25, 78, 2334, ss498763760, ss663198146, ss666079955, ss974768773, ss1367645216, ss1573867000, ss2750604475, ss2986142050, ss3726715213, ss5142033027 NC_000001.10:63735:CTA: NC_000001.11:63735:CTACTA:CTA (self)
5458, 693, ss3063573409, ss3066322496, ss3685990409, ss3798742489, ss3943622692 NC_000001.11:63735:CTA: NC_000001.11:63735:CTACTA:CTA (self)
9943963026 NC_000001.11:63735:CTACTA:CTA NC_000001.11:63735:CTACTA:CTA
ss104663000 NT_077402.2:53737:ACT: NC_000001.11:63735:CTACTA:CTA (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 rs61158452

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