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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.

rs1491102966

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr12:52052328-52052330 (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
delAA
Variation Type
Indel Insertion and Deletion
Frequency
delAA=0.002248 (311/138364, GnomAD)
delAA=0.00061 (10/16330, ALFA)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
NR4A1 : Intron Variant
LOC107984510 : 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 12 NC_000012.12:g.52052329_52052330del
GRCh37.p13 chr 12 NC_000012.11:g.52446113_52446114del
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.38-1998_…

NM_001202233.2:c.38-1998_38-1997del

N/A Intron Variant
NR4A1 transcript variant 4 NM_001202234.2:c.161-1998…

NM_001202234.2:c.161-1998_161-1997del

N/A Intron Variant
NR4A1 transcript variant 1 NM_002135.5:c.-152-167_-1…

NM_002135.5:c.-152-167_-152-166del

N/A Intron Variant
NR4A1 transcript variant 2 NM_173157.3:c.-3+761_-3+7…

NM_173157.3:c.-3+761_-3+762del

N/A Intron Variant
NR4A1 transcript variant X1 XM_005268822.3:c.215-1998…

XM_005268822.3:c.215-1998_215-1997del

N/A Intron Variant
NR4A1 transcript variant X4 XM_005268824.3:c.-2-1998_…

XM_005268824.3:c.-2-1998_-2-1997del

N/A Intron Variant
NR4A1 transcript variant X3 XM_006719363.1:c.-152-167…

XM_006719363.1:c.-152-167_-152-166del

N/A Intron Variant
NR4A1 transcript variant X5 XM_006719364.4:c.-2-1998_…

XM_006719364.4:c.-2-1998_-2-1997del

N/A Intron Variant
NR4A1 transcript variant X2 XM_017019247.1:c.10+656_1…

XM_017019247.1:c.10+656_10+657del

N/A Intron Variant
NR4A1 transcript variant X6 XM_017019248.1:c. N/A Genic Downstream Transcript Variant
NR4A1 transcript variant X7 XM_017019249.1:c. N/A Genic Downstream Transcript Variant
Gene: LOC107984510, uncharacterized LOC107984510 (minus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
LOC107984510 transcript XR_001749148.2:n. 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 16330 AAA=0.99939 A=0.00061
European Sub 12078 AAA=0.99942 A=0.00058
African Sub 2816 AAA=0.9993 A=0.0007
African Others Sub 108 AAA=1.000 A=0.000
African American Sub 2708 AAA=0.9993 A=0.0007
Asian Sub 108 AAA=1.000 A=0.000
East Asian Sub 84 AAA=1.00 A=0.00
Other Asian Sub 24 AAA=1.00 A=0.00
Latin American 1 Sub 146 AAA=1.000 A=0.000
Latin American 2 Sub 610 AAA=1.000 A=0.000
South Asian Sub 94 AAA=1.00 A=0.00
Other Sub 478 AAA=0.998 A=0.002


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 138364 AAA=0.997752 delAA=0.002248
gnomAD - Genomes European Sub 75566 AAA=0.99815 delAA=0.00185
gnomAD - Genomes African Sub 40710 AAA=0.99605 delAA=0.00395
gnomAD - Genomes American Sub 13538 AAA=0.99941 delAA=0.00059
gnomAD - Genomes Ashkenazi Jewish Sub 3316 AAA=1.0000 delAA=0.0000
gnomAD - Genomes East Asian Sub 3108 AAA=1.0000 delAA=0.0000
gnomAD - Genomes Other Sub 2126 AAA=0.9991 delAA=0.0009
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 AAA= delAA
GRCh38.p13 chr 12 NC_000012.12:g.52052328_52052330= NC_000012.12:g.52052329_52052330del
GRCh37.p13 chr 12 NC_000012.11:g.52446112_52446114= NC_000012.11:g.52446113_52446114del
NR4A1 transcript variant 3 NM_001202233.1:c.38-1999= NM_001202233.1:c.38-1998_38-1997del
NR4A1 transcript variant 3 NM_001202233.2:c.38-1999= NM_001202233.2:c.38-1998_38-1997del
NR4A1 transcript variant 4 NM_001202234.2:c.161-1999= NM_001202234.2:c.161-1998_161-1997del
NR4A1 transcript variant 1 NM_002135.4:c.-152-168= NM_002135.4:c.-152-167_-152-166del
NR4A1 transcript variant 1 NM_002135.5:c.-152-168= NM_002135.5:c.-152-167_-152-166del
NR4A1 transcript variant 2 NM_173157.2:c.-3+760= NM_173157.2:c.-3+761_-3+762del
NR4A1 transcript variant 2 NM_173157.3:c.-3+760= NM_173157.3:c.-3+761_-3+762del
NR4A1 transcript variant X1 XM_005268822.1:c.215-1999= XM_005268822.1:c.215-1998_215-1997del
NR4A1 transcript variant X1 XM_005268822.3:c.215-1999= XM_005268822.3:c.215-1998_215-1997del
NR4A1 transcript variant X2 XM_005268823.1:c.161-1999= XM_005268823.1:c.161-1998_161-1997del
NR4A1 transcript variant X3 XM_005268824.1:c.-2-1999= XM_005268824.1:c.-2-1998_-2-1997del
NR4A1 transcript variant X4 XM_005268824.3:c.-2-1999= XM_005268824.3:c.-2-1998_-2-1997del
NR4A1 transcript variant X3 XM_006719363.1:c.-152-168= XM_006719363.1:c.-152-167_-152-166del
NR4A1 transcript variant X5 XM_006719364.4:c.-2-1999= XM_006719364.4:c.-2-1998_-2-1997del
NR4A1 transcript variant X2 XM_017019247.1:c.10+655= XM_017019247.1:c.10+656_10+657del
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, 2 Frequency submissions
No Submitter Submission ID Date (Build)
1 TOPMED ss3170960919 Jan 10, 2018 (151)
2 GNOMAD ss4251849871 Apr 26, 2021 (155)
3 gnomAD - Genomes NC_000012.12 - 52052328 Apr 26, 2021 (155)
4 ALFA NC_000012.12 - 52052328 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
407413873, ss3170960919, ss4251849871 NC_000012.12:52052327:AA: NC_000012.12:52052327:AAA:A (self)
8046556415 NC_000012.12:52052327:AAA:A NC_000012.12:52052327:AAA:A
Removed from this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Destination RSIDs
157681697 NC_000012.11:52446111:AA: NC_000012.12:52052327:AAA:A
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 rs1491102966

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