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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.

rs1491165866

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr12:52028202-52028203 (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
delCA
Variation Type
Deletion
Frequency
delCA=0.00000 (0/11862, ALFA)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
NR4A1 : 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 12 NC_000012.12:g.52028202_52028203del
GRCh37.p13 chr 12 NC_000012.11:g.52421986_52421987del
Gene: NR4A1, nuclear receptor subfamily 4 group A member 1 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
NR4A1 transcript variant 3 NM_001202233.2:c.-84+5263…

NM_001202233.2:c.-84+5263_-84+5264del

N/A Intron Variant
NR4A1 transcript variant 4 NM_001202234.2:c. N/A Genic Upstream Transcript Variant
NR4A1 transcript variant 1 NM_002135.5:c. N/A Genic Upstream Transcript Variant
NR4A1 transcript variant 2 NM_173157.3:c. N/A Genic Upstream Transcript Variant
NR4A1 transcript variant X1 XM_005268822.3:c. N/A Genic Upstream Transcript Variant
NR4A1 transcript variant X4 XM_005268824.3:c. N/A Genic Upstream Transcript Variant
NR4A1 transcript variant X3 XM_006719363.1:c. N/A Genic Upstream Transcript Variant
NR4A1 transcript variant X5 XM_006719364.4:c. N/A Genic Upstream Transcript Variant
NR4A1 transcript variant X2 XM_017019247.1:c. N/A Genic Upstream Transcript Variant
NR4A1 transcript variant X6 XM_017019248.1:c. N/A Genic Upstream Transcript Variant
NR4A1 transcript variant X7 XM_017019249.1:c. N/A Genic 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 11862 CA=1.00000 =0.00000
European Sub 7618 CA=1.0000 =0.0000
African Sub 2816 CA=1.0000 =0.0000
African Others Sub 108 CA=1.000 =0.000
African American Sub 2708 CA=1.0000 =0.0000
Asian Sub 108 CA=1.000 =0.000
East Asian Sub 84 CA=1.00 =0.00
Other Asian Sub 24 CA=1.00 =0.00
Latin American 1 Sub 146 CA=1.000 =0.000
Latin American 2 Sub 610 CA=1.000 =0.000
South Asian Sub 94 CA=1.00 =0.00
Other Sub 470 CA=1.000 =0.000


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
Allele Frequency Aggregator Total Global 11862 CA=1.00000 delCA=0.00000
Allele Frequency Aggregator European Sub 7618 CA=1.0000 delCA=0.0000
Allele Frequency Aggregator African Sub 2816 CA=1.0000 delCA=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 CA=1.000 delCA=0.000
Allele Frequency Aggregator Other Sub 470 CA=1.000 delCA=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 CA=1.000 delCA=0.000
Allele Frequency Aggregator Asian Sub 108 CA=1.000 delCA=0.000
Allele Frequency Aggregator South Asian Sub 94 CA=1.00 delCA=0.00
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 CA= delCA
GRCh38.p13 chr 12 NC_000012.12:g.52028202_52028203= NC_000012.12:g.52028202_52028203del
GRCh37.p13 chr 12 NC_000012.11:g.52421986_52421987= NC_000012.11:g.52421986_52421987del
NR4A1 transcript variant 3 NM_001202233.1:c.-84+5263= NM_001202233.1:c.-84+5263_-84+5264del
NR4A1 transcript variant 3 NM_001202233.2:c.-84+5263= NM_001202233.2:c.-84+5263_-84+5264del
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#.

2 SubSNP, 1 Frequency submissions
No Submitter Submission ID Date (Build)
1 TOPMED ss3170956059 Jan 10, 2018 (151)
2 EVA_DECODE ss3693675148 Jul 13, 2019 (153)
3 ALFA NC_000012.12 - 52028202 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
1655763382, ss3170956059, ss3693675148 NC_000012.12:52028201:CA: NC_000012.12:52028201:CA: (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 rs1491165866

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