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dbSNP Short Genetic Variations

Examples: rs268, BRCA1 and more Advanced search

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.

rs1440403043

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr1:81514689-81514694 (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
delCTT
Variation Type
Indel Insertion and Deletion
Frequency
delCTT=0.000011 (3/264690, TOPMED)
delCTT=0.000007 (1/140178, GnomAD)
delCTT=0.00000 (0/14050, ALFA)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
ADGRL2 : Intron Variant
LOC101927434 : Non Coding Transcript 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 14050 CTTCTT=1.00000 CTT=0.00000 1.0 0.0 0.0 N/A
European Sub 9690 CTTCTT=1.0000 CTT=0.0000 1.0 0.0 0.0 N/A
African Sub 2898 CTTCTT=1.0000 CTT=0.0000 1.0 0.0 0.0 N/A
African Others Sub 114 CTTCTT=1.000 CTT=0.000 1.0 0.0 0.0 N/A
African American Sub 2784 CTTCTT=1.0000 CTT=0.0000 1.0 0.0 0.0 N/A
Asian Sub 112 CTTCTT=1.000 CTT=0.000 1.0 0.0 0.0 N/A
East Asian Sub 86 CTTCTT=1.00 CTT=0.00 1.0 0.0 0.0 N/A
Other Asian Sub 26 CTTCTT=1.00 CTT=0.00 1.0 0.0 0.0 N/A
Latin American 1 Sub 146 CTTCTT=1.000 CTT=0.000 1.0 0.0 0.0 N/A
Latin American 2 Sub 610 CTTCTT=1.000 CTT=0.000 1.0 0.0 0.0 N/A
South Asian Sub 98 CTTCTT=1.00 CTT=0.00 1.0 0.0 0.0 N/A
Other Sub 496 CTTCTT=1.000 CTT=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
TopMed Global Study-wide 264690 (CTT)2=0.999989 delCTT=0.000011
gnomAD - Genomes Global Study-wide 140178 (CTT)2=0.999993 delCTT=0.000007
gnomAD - Genomes European Sub 75914 (CTT)2=1.00000 delCTT=0.00000
gnomAD - Genomes African Sub 42022 (CTT)2=0.99998 delCTT=0.00002
gnomAD - Genomes American Sub 13636 (CTT)2=1.00000 delCTT=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3320 (CTT)2=1.0000 delCTT=0.0000
gnomAD - Genomes East Asian Sub 3134 (CTT)2=1.0000 delCTT=0.0000
gnomAD - Genomes Other Sub 2152 (CTT)2=1.0000 delCTT=0.0000
Allele Frequency Aggregator Total Global 14050 (CTT)2=1.00000 delCTT=0.00000
Allele Frequency Aggregator European Sub 9690 (CTT)2=1.0000 delCTT=0.0000
Allele Frequency Aggregator African Sub 2898 (CTT)2=1.0000 delCTT=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 (CTT)2=1.000 delCTT=0.000
Allele Frequency Aggregator Other Sub 496 (CTT)2=1.000 delCTT=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 (CTT)2=1.000 delCTT=0.000
Allele Frequency Aggregator Asian Sub 112 (CTT)2=1.000 delCTT=0.000
Allele Frequency Aggregator South Asian Sub 98 (CTT)2=1.00 delCTT=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.81514689CTT[1]
GRCh37.p13 chr 1 NC_000001.10:g.81980374CTT[1]
Gene: ADGRL2, adhesion G protein-coupled receptor L2 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
ADGRL2 transcript variant 9 NM_001366003.2:c.-309-661…

NM_001366003.2:c.-309-66184_-309-66182del

 		N/A Intron Variant
ADGRL2 transcript variant 10 NM_001366004.2:c.-309-661…

NM_001366004.2:c.-309-66184_-309-66182del

 		N/A Intron Variant
ADGRL2 transcript variant 14 NM_001366008.2:c.-247-661…

NM_001366008.2:c.-247-66184_-247-66182del

 		N/A Intron Variant
ADGRL2 transcript variant 16 NM_001393349.1:c.-247-661…

NM_001393349.1:c.-247-66184_-247-66182del

 		N/A Intron Variant
ADGRL2 transcript variant 2 NM_001297704.3:c. N/A Genic Upstream Transcript Variant
ADGRL2 transcript variant 3 NM_001297705.3:c. N/A Genic Upstream Transcript Variant
ADGRL2 transcript variant 4 NM_001297706.3:c. N/A Genic Upstream Transcript Variant
ADGRL2 transcript variant 5 NM_001330645.3:c. N/A Genic Upstream Transcript Variant
ADGRL2 transcript variant 6 NM_001350698.2:c. N/A Genic Upstream Transcript Variant
ADGRL2 transcript variant 7 NM_001350699.2:c. N/A Genic Upstream Transcript Variant
ADGRL2 transcript variant 8 NM_001366002.2:c. N/A Genic Upstream Transcript Variant
ADGRL2 transcript variant 11 NM_001366005.2:c. N/A Genic Upstream Transcript Variant
ADGRL2 transcript variant 12 NM_001366006.2:c. N/A Genic Upstream Transcript Variant
ADGRL2 transcript variant 13 NM_001366007.2:c. N/A Genic Upstream Transcript Variant
ADGRL2 transcript variant 15 NM_001366009.2:c. N/A Genic Upstream Transcript Variant
ADGRL2 transcript variant 17 NM_001393350.1:c. N/A Genic Upstream Transcript Variant
ADGRL2 transcript variant 18 NM_001393351.1:c. N/A Genic Upstream Transcript Variant
ADGRL2 transcript variant 19 NM_001393352.1:c. N/A Genic Upstream Transcript Variant
ADGRL2 transcript variant 20 NM_001393353.1:c. N/A Genic Upstream Transcript Variant
ADGRL2 transcript variant 21 NM_001393354.1:c. N/A Genic Upstream Transcript Variant
ADGRL2 transcript variant 1 NM_012302.5:c. N/A Genic Upstream Transcript Variant
ADGRL2 transcript variant 22 NR_171658.1:n. N/A Genic Upstream Transcript Variant
ADGRL2 transcript variant X16 XM_047416118.1:c.-398-661…

XM_047416118.1:c.-398-66184_-398-66182del

 		N/A Intron Variant
ADGRL2 transcript variant X29 XM_047416140.1:c.-398-661…

XM_047416140.1:c.-398-66184_-398-66182del

 		N/A Intron Variant
ADGRL2 transcript variant X34 XM_047416152.1:c.-398-661…

XM_047416152.1:c.-398-66184_-398-66182del

 		N/A Intron Variant
ADGRL2 transcript variant X36 XM_047416159.1:c.-398-661…

XM_047416159.1:c.-398-66184_-398-66182del

 		N/A Intron Variant
ADGRL2 transcript variant X12 XM_005270666.5:c. N/A Genic Upstream Transcript Variant
ADGRL2 transcript variant X18 XM_005270668.3:c. N/A Genic Upstream Transcript Variant
ADGRL2 transcript variant X1 XM_006710485.4:c. N/A Genic Upstream Transcript Variant
ADGRL2 transcript variant X2 XM_006710488.3:c. N/A Genic Upstream Transcript Variant
ADGRL2 transcript variant X4 XM_006710489.4:c. N/A Genic Upstream Transcript Variant
ADGRL2 transcript variant X6 XM_017000784.2:c. N/A Genic Upstream Transcript Variant
ADGRL2 transcript variant X26 XM_024454355.2:c. N/A Genic Upstream Transcript Variant
ADGRL2 transcript variant X3 XM_047416092.1:c. N/A Genic Upstream Transcript Variant
ADGRL2 transcript variant X5 XM_047416096.1:c. N/A Genic Upstream Transcript Variant
ADGRL2 transcript variant X7 XM_047416098.1:c. N/A Genic Upstream Transcript Variant
ADGRL2 transcript variant X8 XM_047416099.1:c. N/A Genic Upstream Transcript Variant
ADGRL2 transcript variant X9 XM_047416102.1:c. N/A Genic Upstream Transcript Variant
ADGRL2 transcript variant X10 XM_047416104.1:c. N/A Genic Upstream Transcript Variant
ADGRL2 transcript variant X11 XM_047416105.1:c. N/A Genic Upstream Transcript Variant
ADGRL2 transcript variant X13 XM_047416109.1:c. N/A Genic Upstream Transcript Variant
ADGRL2 transcript variant X14 XM_047416110.1:c. N/A Genic Upstream Transcript Variant
ADGRL2 transcript variant X15 XM_047416115.1:c. N/A Genic Upstream Transcript Variant
ADGRL2 transcript variant X17 XM_047416119.1:c. N/A Genic Upstream Transcript Variant
ADGRL2 transcript variant X19 XM_047416120.1:c. N/A Genic Upstream Transcript Variant
ADGRL2 transcript variant X20 XM_047416121.1:c. N/A Genic Upstream Transcript Variant
ADGRL2 transcript variant X21 XM_047416124.1:c. N/A Genic Upstream Transcript Variant
ADGRL2 transcript variant X22 XM_047416126.1:c. N/A Genic Upstream Transcript Variant
ADGRL2 transcript variant X23 XM_047416128.1:c. N/A Genic Upstream Transcript Variant
ADGRL2 transcript variant X24 XM_047416129.1:c. N/A Genic Upstream Transcript Variant
ADGRL2 transcript variant X25 XM_047416130.1:c. N/A Genic Upstream Transcript Variant
ADGRL2 transcript variant X27 XM_047416132.1:c. N/A Genic Upstream Transcript Variant
ADGRL2 transcript variant X28 XM_047416136.1:c. N/A Genic Upstream Transcript Variant
ADGRL2 transcript variant X30 XM_047416145.1:c. N/A Genic Upstream Transcript Variant
ADGRL2 transcript variant X31 XM_047416146.1:c. N/A Genic Upstream Transcript Variant
ADGRL2 transcript variant X32 XM_047416148.1:c. N/A Genic Upstream Transcript Variant
ADGRL2 transcript variant X33 XM_047416150.1:c. N/A Genic Upstream Transcript Variant
ADGRL2 transcript variant X35 XM_047416156.1:c. N/A Genic Upstream Transcript Variant
ADGRL2 transcript variant X37 XM_047416164.1:c. N/A Genic Upstream Transcript Variant
ADGRL2 transcript variant X38 XM_047416170.1:c. N/A Genic Upstream Transcript Variant
ADGRL2 transcript variant X39 XM_047416176.1:c. N/A Genic Upstream Transcript Variant
ADGRL2 transcript variant X40 XM_047416178.1:c. N/A Genic Upstream Transcript Variant
ADGRL2 transcript variant X41 XM_047416180.1:c. N/A Genic Upstream Transcript Variant
Gene: LOC101927434, uncharacterized LOC101927434 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
LOC101927434 transcript NR_125943.1:n.413AAG[1] N/A Non Coding 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
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 (CTT)2= delCTT
GRCh38.p14 chr 1 NC_000001.11:g.81514689_81514694= NC_000001.11:g.81514689CTT[1]
GRCh37.p13 chr 1 NC_000001.10:g.81980374_81980379= NC_000001.10:g.81980374CTT[1]
LOC101927434 transcript NR_125943.1:n.413_418= NR_125943.1:n.413AAG[1]
ADGRL2 transcript variant 9 NM_001366003.2:c.-309-66187= NM_001366003.2:c.-309-66184_-309-66182del
ADGRL2 transcript variant 10 NM_001366004.2:c.-309-66187= NM_001366004.2:c.-309-66184_-309-66182del
ADGRL2 transcript variant 14 NM_001366008.2:c.-247-66187= NM_001366008.2:c.-247-66184_-247-66182del
ADGRL2 transcript variant 16 NM_001393349.1:c.-247-66187= NM_001393349.1:c.-247-66184_-247-66182del
ADGRL2 transcript variant X16 XM_047416118.1:c.-398-66187= XM_047416118.1:c.-398-66184_-398-66182del
ADGRL2 transcript variant X29 XM_047416140.1:c.-398-66187= XM_047416140.1:c.-398-66184_-398-66182del
ADGRL2 transcript variant X34 XM_047416152.1:c.-398-66187= XM_047416152.1:c.-398-66184_-398-66182del
ADGRL2 transcript variant X36 XM_047416159.1:c.-398-66187= XM_047416159.1:c.-398-66184_-398-66182del
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, 3 Frequency submissions
No Submitter Submission ID Date (Build)
1 GNOMAD ss3996858639 Apr 27, 2021 (155)
2 TOPMED ss4456298973 Apr 27, 2021 (155)
3 gnomAD - Genomes NC_000001.11 - 81514689 Apr 27, 2021 (155)
4 TopMed NC_000001.11 - 81514689 Apr 27, 2021 (155)
5 ALFA NC_000001.11 - 81514689 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
16735015, 19905308, ss3996858639, ss4456298973 NC_000001.11:81514688:CTT: NC_000001.11:81514688:CTTCTT:CTT (self)
12972718630 NC_000001.11:81514688:CTTCTT:CTT NC_000001.11:81514688:CTTCTT:CTT (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 rs1440403043

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