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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.

rs1491099667

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr11:111512396-111512397 (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
delAT
Variation Type
Deletion
Frequency
delAT=0.00057 (16/28256, 14KJPN)
delAT=0.0020 (9/4470, ALFA)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
BTG4 : Intron Variant
MIR34BHG : Intron Variant
MIR34B : 2KB Upstream Variant (+ 1 more)
MIR34C : 2KB Upstream 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 4470 AT=0.9980 =0.0020 0.996421 0.000447 0.003132 32
European Sub 4462 AT=0.9980 =0.0020 0.996414 0.000448 0.003138 32
African Sub 0 AT=0 =0 0 0 0 N/A
African Others Sub 0 AT=0 =0 0 0 0 N/A
African American Sub 0 AT=0 =0 0 0 0 N/A
Asian Sub 0 AT=0 =0 0 0 0 N/A
East Asian Sub 0 AT=0 =0 0 0 0 N/A
Other Asian Sub 0 AT=0 =0 0 0 0 N/A
Latin American 1 Sub 0 AT=0 =0 0 0 0 N/A
Latin American 2 Sub 0 AT=0 =0 0 0 0 N/A
South Asian Sub 0 AT=0 =0 0 0 0 N/A
Other Sub 8 AT=1.0 =0.0 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
14KJPN JAPANESE Study-wide 28256 AT=0.99943 delAT=0.00057
Allele Frequency Aggregator Total Global 4470 AT=0.9980 delAT=0.0020
Allele Frequency Aggregator European Sub 4462 AT=0.9980 delAT=0.0020
Allele Frequency Aggregator Other Sub 8 AT=1.0 delAT=0.0
Allele Frequency Aggregator Latin American 1 Sub 0 AT=0 delAT=0
Allele Frequency Aggregator Latin American 2 Sub 0 AT=0 delAT=0
Allele Frequency Aggregator South Asian Sub 0 AT=0 delAT=0
Allele Frequency Aggregator African Sub 0 AT=0 delAT=0
Allele Frequency Aggregator Asian Sub 0 AT=0 delAT=0
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 11 NC_000011.10:g.111512396_111512397del
GRCh37.p13 chr 11 NC_000011.9:g.111383121_111383122del
Gene: BTG4, BTG anti-proliferation factor 4 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
BTG4 transcript variant 2 NM_001367974.1:c.-27+2270…

NM_001367974.1:c.-27+2270_-27+2271del

 		N/A Intron Variant
BTG4 transcript variant 3 NM_001367975.1:c. N/A Genic Upstream Transcript Variant
BTG4 transcript variant 4 NM_001367976.1:c. N/A Genic Upstream Transcript Variant
BTG4 transcript variant 1 NM_017589.4:c. N/A Genic Upstream Transcript Variant
BTG4 transcript variant X3 XM_024448589.2:c.-27+2270…

XM_024448589.2:c.-27+2270_-27+2271del

 		N/A Intron Variant
BTG4 transcript variant X5 XM_024448591.2:c.-27+1821…

XM_024448591.2:c.-27+1821_-27+1822del

 		N/A Intron Variant
BTG4 transcript variant X8 XM_011542876.3:c. N/A Genic Upstream Transcript Variant
BTG4 transcript variant X14 XM_011542879.3:c. N/A Genic Upstream Transcript Variant
BTG4 transcript variant X16 XM_011542880.3:c. N/A Genic Upstream Transcript Variant
BTG4 transcript variant X1 XM_024448587.2:c. N/A Genic Upstream Transcript Variant
BTG4 transcript variant X2 XM_024448588.2:c. N/A Genic Upstream Transcript Variant
BTG4 transcript variant X4 XM_024448590.2:c. N/A Genic Upstream Transcript Variant
BTG4 transcript variant X9 XM_024448592.2:c. N/A Genic Upstream Transcript Variant
BTG4 transcript variant X15 XR_001747911.3:n. N/A Genic Upstream Transcript Variant
BTG4 transcript variant X10 XR_007062488.1:n. N/A Genic Upstream Transcript Variant
BTG4 transcript variant X7 XR_947834.3:n. N/A Genic Upstream Transcript Variant
BTG4 transcript variant X6 XR_947835.3:n. N/A Genic Upstream Transcript Variant
BTG4 transcript variant X11 XR_947849.3:n. N/A Genic Upstream Transcript Variant
BTG4 transcript variant X12 XR_947851.3:n. N/A Genic Upstream Transcript Variant
BTG4 transcript variant X13 XR_947852.3:n. N/A Genic Upstream Transcript Variant
BTG4 transcript variant X17 XR_947855.3:n. N/A Genic Upstream Transcript Variant
Gene: MIR34BHG, MIR34B and MIR34C host gene (plus strand)
Molecule type Change Amino acid[Codon] SO Term
MIR34BHG transcript NR_147706.1:n. N/A Intron Variant
Gene: MIR34B, microRNA 34b (plus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
MIR34B transcript NR_029839.1:n. N/A Upstream Transcript Variant
Gene: MIR34C, microRNA 34c (plus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
MIR34C transcript NR_029840.1: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
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 AT= delAT
GRCh38.p14 chr 11 NC_000011.10:g.111512396_111512397= NC_000011.10:g.111512396_111512397del
GRCh37.p13 chr 11 NC_000011.9:g.111383121_111383122= NC_000011.9:g.111383121_111383122del
BTG4 transcript variant 2 NM_001367974.1:c.-27+2271= NM_001367974.1:c.-27+2270_-27+2271del
BTG4 transcript variant X3 XM_024448589.2:c.-27+2271= XM_024448589.2:c.-27+2270_-27+2271del
BTG4 transcript variant X5 XM_024448591.2:c.-27+1822= XM_024448591.2:c.-27+1821_-27+1822del
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#.

1 SubSNP, 2 Frequency submissions
No Submitter Submission ID Date (Build)
1 TOMMO_GENOMICS ss5752349142 Oct 16, 2022 (156)
2 14KJPN NC_000011.10 - 111512396 Oct 16, 2022 (156)
3 ALFA NC_000011.10 - 111512396 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
86186246, 6295197448, ss5752349142 NC_000011.10:111512395:AT: NC_000011.10:111512395:AT: (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 rs1491099667

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