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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.

rs1491433914

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr1:28846894-28846898 (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
delCTCT / delCT
Variation Type
Indel Insertion and Deletion
Frequency
delCT=0.03662 (1592/43476, GnomAD)
delCT=0.00225 (26/11546, ALFA)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
OPRD1 : 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: 20231103111315
Population Group Sample Size Ref Allele Alt Allele Ref HMOZ Alt HMOZ HTRZ HWEP
Total Global 11546 TCTCT=0.99775 T=0.00000, TCT=0.00225 0.995496 0.0 0.004504 0
European Sub 7614 TCTCT=1.0000 T=0.0000, TCT=0.0000 1.0 0.0 0.0 N/A
African Sub 2534 TCTCT=0.9897 T=0.0000, TCT=0.0103 0.979479 0.0 0.020521 0
African Others Sub 98 TCTCT=0.98 T=0.00, TCT=0.02 0.959184 0.0 0.040816 0
African American Sub 2436 TCTCT=0.9901 T=0.0000, TCT=0.0099 0.980296 0.0 0.019704 0
Asian Sub 108 TCTCT=1.000 T=0.000, TCT=0.000 1.0 0.0 0.0 N/A
East Asian Sub 84 TCTCT=1.00 T=0.00, TCT=0.00 1.0 0.0 0.0 N/A
Other Asian Sub 24 TCTCT=1.00 T=0.00, TCT=0.00 1.0 0.0 0.0 N/A
Latin American 1 Sub 142 TCTCT=1.000 T=0.000, TCT=0.000 1.0 0.0 0.0 N/A
Latin American 2 Sub 604 TCTCT=1.000 T=0.000, TCT=0.000 1.0 0.0 0.0 N/A
South Asian Sub 94 TCTCT=1.00 T=0.00, TCT=0.00 1.0 0.0 0.0 N/A
Other Sub 450 TCTCT=1.000 T=0.000, TCT=0.000 1.0 0.0 0.0 N/A


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 43476 TCTCT=0.96338 delCT=0.03662
gnomAD - Genomes African Sub 21700 TCTCT=0.92972 delCT=0.07028
gnomAD - Genomes European Sub 16934 TCTCT=0.99941 delCT=0.00059
gnomAD - Genomes American Sub 3378 TCTCT=0.9873 delCT=0.0127
gnomAD - Genomes Ashkenazi Jewish Sub 772 TCTCT=1.000 delCT=0.000
gnomAD - Genomes Other Sub 588 TCTCT=0.976 delCT=0.024
gnomAD - Genomes East Asian Sub 104 TCTCT=1.000 delCT=0.000
Allele Frequency Aggregator Total Global 11546 TCTCT=0.99775 delCTCT=0.00000, delCT=0.00225
Allele Frequency Aggregator European Sub 7614 TCTCT=1.0000 delCTCT=0.0000, delCT=0.0000
Allele Frequency Aggregator African Sub 2534 TCTCT=0.9897 delCTCT=0.0000, delCT=0.0103
Allele Frequency Aggregator Latin American 2 Sub 604 TCTCT=1.000 delCTCT=0.000, delCT=0.000
Allele Frequency Aggregator Other Sub 450 TCTCT=1.000 delCTCT=0.000, delCT=0.000
Allele Frequency Aggregator Latin American 1 Sub 142 TCTCT=1.000 delCTCT=0.000, delCT=0.000
Allele Frequency Aggregator Asian Sub 108 TCTCT=1.000 delCTCT=0.000, delCT=0.000
Allele Frequency Aggregator South Asian Sub 94 TCTCT=1.00 delCTCT=0.00, delCT=0.00
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 1 NC_000001.11:g.28846895_28846898del
GRCh38.p14 chr 1 NC_000001.11:g.28846895CT[1]
GRCh37.p13 chr 1 NC_000001.10:g.29173407_29173410del
GRCh37.p13 chr 1 NC_000001.10:g.29173407CT[1]
Gene: OPRD1, opioid receptor delta 1 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
OPRD1 transcript NM_000911.4:c.228-12059_2…

NM_000911.4:c.228-12059_228-12056del

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 TCTCT= delCTCT delCT
GRCh38.p14 chr 1 NC_000001.11:g.28846894_28846898= NC_000001.11:g.28846895_28846898del NC_000001.11:g.28846895CT[1]
GRCh37.p13 chr 1 NC_000001.10:g.29173406_29173410= NC_000001.10:g.29173407_29173410del NC_000001.10:g.29173407CT[1]
OPRD1 transcript NM_000911.3:c.228-12060= NM_000911.3:c.228-12059_228-12056del NM_000911.3:c.228-12057_228-12056del
OPRD1 transcript NM_000911.4:c.228-12060= NM_000911.4:c.228-12059_228-12056del NM_000911.4:c.228-12057_228-12056del
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#.

5 SubSNP, 2 Frequency submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss498816260 Jan 10, 2018 (151)
2 GNOMAD ss3990519443 Apr 27, 2021 (155)
3 1000G_HIGH_COVERAGE ss5241644536 Oct 13, 2022 (156)
4 HUGCELL_USP ss5442777701 Oct 13, 2022 (156)
5 EVA ss5936999813 Oct 13, 2022 (156)
6 gnomAD - Genomes NC_000001.11 - 28846894 Apr 27, 2021 (155)
7 ALFA NC_000001.11 - 28846894 Apr 27, 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
9626078559 NC_000001.11:28846893:TCTCT:T NC_000001.11:28846893:TCTCT:T (self)
ss498816260, ss5936999813 NC_000001.10:29173405:TC: NC_000001.11:28846893:TCTCT:TCT (self)
6178191, ss3990519443, ss5241644536, ss5442777701 NC_000001.11:28846893:TC: NC_000001.11:28846893:TCTCT:TCT (self)
9626078559 NC_000001.11:28846893:TCTCT:TCT NC_000001.11:28846893:TCTCT:TCT (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 rs1491433914

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.post820+afb47a3d