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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.

rs1459379639

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr1:11655889-11655896 (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
delCACG
Variation Type
Indel Insertion and Deletion
Frequency
delCACG=0.000004 (1/264690, TOPMED)
delCACG=0.00000 (0/11862, ALFA)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
FBXO44 : Frameshift Variant
FBXO2 : 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 11862 CACGCACG=1.00000 CACG=0.00000 1.0 0.0 0.0 N/A
European Sub 7618 CACGCACG=1.0000 CACG=0.0000 1.0 0.0 0.0 N/A
African Sub 2816 CACGCACG=1.0000 CACG=0.0000 1.0 0.0 0.0 N/A
African Others Sub 108 CACGCACG=1.000 CACG=0.000 1.0 0.0 0.0 N/A
African American Sub 2708 CACGCACG=1.0000 CACG=0.0000 1.0 0.0 0.0 N/A
Asian Sub 108 CACGCACG=1.000 CACG=0.000 1.0 0.0 0.0 N/A
East Asian Sub 84 CACGCACG=1.00 CACG=0.00 1.0 0.0 0.0 N/A
Other Asian Sub 24 CACGCACG=1.00 CACG=0.00 1.0 0.0 0.0 N/A
Latin American 1 Sub 146 CACGCACG=1.000 CACG=0.000 1.0 0.0 0.0 N/A
Latin American 2 Sub 610 CACGCACG=1.000 CACG=0.000 1.0 0.0 0.0 N/A
South Asian Sub 94 CACGCACG=1.00 CACG=0.00 1.0 0.0 0.0 N/A
Other Sub 470 CACGCACG=1.000 CACG=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 (CACG)2=0.999996 delCACG=0.000004
Allele Frequency Aggregator Total Global 11862 (CACG)2=1.00000 delCACG=0.00000
Allele Frequency Aggregator European Sub 7618 (CACG)2=1.0000 delCACG=0.0000
Allele Frequency Aggregator African Sub 2816 (CACG)2=1.0000 delCACG=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 (CACG)2=1.000 delCACG=0.000
Allele Frequency Aggregator Other Sub 470 (CACG)2=1.000 delCACG=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 (CACG)2=1.000 delCACG=0.000
Allele Frequency Aggregator Asian Sub 108 (CACG)2=1.000 delCACG=0.000
Allele Frequency Aggregator South Asian Sub 94 (CACG)2=1.00 delCACG=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.11655889CACG[1]
GRCh37.p13 chr 1 NC_000001.10:g.11715946CACG[1]
Gene: FBXO2, F-box protein 2 (minus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
FBXO2 transcript NM_012168.6:c. N/A Upstream Transcript Variant
Gene: FBXO44, F-box protein 44 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
FBXO44 transcript variant 2 NM_183412.3:c.58_61del H [CAC] > C [TG] Coding Sequence Variant
F-box only protein 44 isoform 2 NP_904319.1:p.His20fs H (His) > C (Cys) Frameshift Variant
FBXO44 transcript variant 6 NM_001304791.2:c.58_61del H [CAC] > C [TG] Coding Sequence Variant
F-box only protein 44 isoform 1 NP_001291720.1:p.His20fs H (His) > C (Cys) Frameshift Variant
FBXO44 transcript variant 1 NM_033182.7:c.58_61del H [CAC] > C [TG] Coding Sequence Variant
F-box only protein 44 isoform 1 NP_149438.2:p.His20fs H (His) > C (Cys) Frameshift Variant
FBXO44 transcript variant 4 NM_001014765.2:c.58_61del H [CAC] > C [TG] Coding Sequence Variant
F-box only protein 44 isoform 1 NP_001014765.1:p.His20fs H (His) > C (Cys) Frameshift Variant
FBXO44 transcript variant 5 NM_001304790.2:c.58_61del H [CAC] > C [TG] Coding Sequence Variant
F-box only protein 44 isoform 2 NP_001291719.1:p.His20fs H (His) > C (Cys) Frameshift Variant
FBXO44 transcript variant 8 NM_001330355.2:c.58_61del H [CAC] > C [TG] Coding Sequence Variant
F-box only protein 44 isoform 3 NP_001317284.1:p.His20fs H (His) > C (Cys) Frameshift Variant
FBXO44 transcript variant 3 NM_183413.3:c.58_61del H [CAC] > C [TG] Coding Sequence Variant
F-box only protein 44 isoform 2 NP_904320.1:p.His20fs H (His) > C (Cys) Frameshift Variant
FBXO44 transcript variant 7 NR_130909.2:n. N/A Intron Variant
FBXO44 transcript variant X11 XM_017002843.2:c.58_61del H [CAC] > C [TG] Coding Sequence Variant
F-box only protein 44 isoform X2 XP_016858332.1:p.His20fs H (His) > C (Cys) Frameshift Variant
FBXO44 transcript variant X1 XM_005263536.5:c.58_61del H [CAC] > C [TG] Coding Sequence Variant
F-box only protein 44 isoform X1 XP_005263593.1:p.His20fs H (His) > C (Cys) Frameshift Variant
FBXO44 transcript variant X2 XM_005263537.2:c.58_61del H [CAC] > C [TG] Coding Sequence Variant
F-box only protein 44 isoform X1 XP_005263594.1:p.His20fs H (His) > C (Cys) Frameshift Variant
FBXO44 transcript variant X3 XM_017002842.3:c.58_61del H [CAC] > C [TG] Coding Sequence Variant
F-box only protein 44 isoform X1 XP_016858331.1:p.His20fs H (His) > C (Cys) Frameshift Variant
FBXO44 transcript variant X4 XM_006711043.4:c.58_61del H [CAC] > C [TG] Coding Sequence Variant
F-box only protein 44 isoform X1 XP_006711106.1:p.His20fs H (His) > C (Cys) Frameshift Variant
FBXO44 transcript variant X6 XM_011542435.2:c.58_61del H [CAC] > C [TG] Coding Sequence Variant
F-box only protein 44 isoform X1 XP_011540737.1:p.His20fs H (His) > C (Cys) Frameshift Variant
FBXO44 transcript variant X7 XM_047434631.1:c.58_61del H [CAC] > C [TG] Coding Sequence Variant
F-box only protein 44 isoform X1 XP_047290587.1:p.His20fs H (His) > C (Cys) Frameshift Variant
FBXO44 transcript variant X8 XM_047434635.1:c.58_61del H [CAC] > C [TG] Coding Sequence Variant
F-box only protein 44 isoform X2 XP_047290591.1:p.His20fs H (His) > C (Cys) Frameshift Variant
FBXO44 transcript variant X10 XM_047434637.1:c.58_61del H [CAC] > C [TG] Coding Sequence Variant
F-box only protein 44 isoform X2 XP_047290593.1:p.His20fs H (His) > C (Cys) Frameshift Variant
FBXO44 transcript variant X12 XM_047434647.1:c.58_61del H [CAC] > C [TG] Coding Sequence Variant
F-box only protein 44 isoform X2 XP_047290603.1:p.His20fs H (His) > C (Cys) Frameshift Variant
FBXO44 transcript variant X13 XM_006711045.4:c.58_61del H [CAC] > C [TG] Coding Sequence Variant
F-box only protein 44 isoform X2 XP_006711108.1:p.His20fs H (His) > C (Cys) Frameshift Variant
FBXO44 transcript variant X15 XM_047434652.1:c.58_61del H [CAC] > C [TG] Coding Sequence Variant
F-box only protein 44 isoform X2 XP_047290608.1:p.His20fs H (His) > C (Cys) Frameshift Variant
FBXO44 transcript variant X16 XM_017002844.3:c.58_61del H [CAC] > C [TG] Coding Sequence Variant
F-box only protein 44 isoform X3 XP_016858333.1:p.His20fs H (His) > C (Cys) Frameshift Variant
FBXO44 transcript variant X17 XM_047434659.1:c.58_61del H [CAC] > C [TG] Coding Sequence Variant
F-box only protein 44 isoform X3 XP_047290615.1:p.His20fs H (His) > C (Cys) Frameshift Variant
FBXO44 transcript variant X19 XM_047434660.1:c.58_61del H [CAC] > C [TG] Coding Sequence Variant
F-box only protein 44 isoform X3 XP_047290616.1:p.His20fs H (His) > C (Cys) Frameshift Variant
FBXO44 transcript variant X5 XR_007064913.1:n.160CACG[…

XR_007064913.1:n.160CACG[1]

 		N/A Non Coding Transcript Variant
FBXO44 transcript variant X9 XR_007064914.1:n.160CACG[…

XR_007064914.1:n.160CACG[1]

 		N/A Non Coding Transcript Variant
FBXO44 transcript variant X14 XR_007064917.1:n.532CACG[…

XR_007064917.1:n.532CACG[1]

 		N/A Non Coding Transcript Variant
FBXO44 transcript variant X18 XR_007064918.1:n.160CACG[…

XR_007064918.1:n.160CACG[1]

 		N/A Non Coding Transcript Variant
FBXO44 transcript variant X20 XR_007064919.1:n.259CACG[…

XR_007064919.1:n.259CACG[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 (CACG)2= delCACG
GRCh38.p14 chr 1 NC_000001.11:g.11655889_11655896= NC_000001.11:g.11655889CACG[1]
GRCh37.p13 chr 1 NC_000001.10:g.11715946_11715953= NC_000001.10:g.11715946CACG[1]
FBXO44 transcript variant 1 NM_033182.7:c.54_61= NM_033182.7:c.58_61del
FBXO44 transcript variant 1 NM_033182.6:c.54_61= NM_033182.6:c.58_61del
FBXO44 transcript variant 1 NM_033182.5:c.54_61= NM_033182.5:c.58_61del
FBXO44 transcript variant X1 XM_005263536.5:c.54_61= XM_005263536.5:c.58_61del
FBXO44 transcript variant X1 XM_005263536.4:c.54_61= XM_005263536.4:c.58_61del
FBXO44 transcript variant X2 XM_005263536.3:c.54_61= XM_005263536.3:c.58_61del
FBXO44 transcript variant X2 XM_005263536.2:c.54_61= XM_005263536.2:c.58_61del
FBXO44 transcript variant X2 XM_005263536.1:c.54_61= XM_005263536.1:c.58_61del
FBXO44 transcript variant X13 XM_006711045.4:c.54_61= XM_006711045.4:c.58_61del
FBXO44 transcript variant X7 XM_006711045.3:c.54_61= XM_006711045.3:c.58_61del
FBXO44 transcript variant X8 XM_006711045.2:c.54_61= XM_006711045.2:c.58_61del
FBXO44 transcript variant X8 XM_006711045.1:c.54_61= XM_006711045.1:c.58_61del
FBXO44 transcript variant X4 XM_006711043.4:c.54_61= XM_006711043.4:c.58_61del
FBXO44 transcript variant X5 XM_006711043.3:c.54_61= XM_006711043.3:c.58_61del
FBXO44 transcript variant X6 XM_006711043.2:c.54_61= XM_006711043.2:c.58_61del
FBXO44 transcript variant X6 XM_006711043.1:c.54_61= XM_006711043.1:c.58_61del
FBXO44 transcript variant 2 NM_183412.3:c.54_61= NM_183412.3:c.58_61del
FBXO44 transcript variant 2 NM_183412.2:c.54_61= NM_183412.2:c.58_61del
FBXO44 transcript variant 3 NM_183413.3:c.54_61= NM_183413.3:c.58_61del
FBXO44 transcript variant 3 NM_183413.2:c.54_61= NM_183413.2:c.58_61del
FBXO44 transcript variant X3 XM_017002842.3:c.54_61= XM_017002842.3:c.58_61del
FBXO44 transcript variant X4 XM_017002842.2:c.54_61= XM_017002842.2:c.58_61del
FBXO44 transcript variant X5 XM_017002842.1:c.54_61= XM_017002842.1:c.58_61del
FBXO44 transcript variant X16 XM_017002844.3:c.54_61= XM_017002844.3:c.58_61del
FBXO44 transcript variant X10 XM_017002844.2:c.54_61= XM_017002844.2:c.58_61del
FBXO44 transcript variant X9 XM_017002844.1:c.54_61= XM_017002844.1:c.58_61del
FBXO44 transcript variant X6 XM_011542435.2:c.54_61= XM_011542435.2:c.58_61del
FBXO44 transcript variant X2 XM_011542435.1:c.54_61= XM_011542435.1:c.58_61del
FBXO44 transcript variant 4 NM_001014765.2:c.54_61= NM_001014765.2:c.58_61del
FBXO44 transcript variant 4 NM_001014765.1:c.54_61= NM_001014765.1:c.58_61del
FBXO44 transcript variant 6 NM_001304791.2:c.54_61= NM_001304791.2:c.58_61del
FBXO44 transcript variant 6 NM_001304791.1:c.54_61= NM_001304791.1:c.58_61del
FBXO44 transcript variant X2 XM_005263537.2:c.54_61= XM_005263537.2:c.58_61del
FBXO44 transcript variant X3 XM_005263537.1:c.54_61= XM_005263537.1:c.58_61del
FBXO44 transcript variant 8 NM_001330355.2:c.54_61= NM_001330355.2:c.58_61del
FBXO44 transcript variant 8 NM_001330355.1:c.54_61= NM_001330355.1:c.58_61del
FBXO44 transcript variant 5 NM_001304790.2:c.54_61= NM_001304790.2:c.58_61del
FBXO44 transcript variant 5 NM_001304790.1:c.54_61= NM_001304790.1:c.58_61del
FBXO44 transcript variant X11 XM_017002843.2:c.54_61= XM_017002843.2:c.58_61del
FBXO44 transcript variant X7 XM_017002843.1:c.54_61= XM_017002843.1:c.58_61del
FBXO44 transcript variant X15 XM_047434652.1:c.54_61= XM_047434652.1:c.58_61del
FBXO44 transcript variant X8 XM_047434635.1:c.54_61= XM_047434635.1:c.58_61del
FBXO44 transcript variant X7 XM_047434631.1:c.54_61= XM_047434631.1:c.58_61del
FBXO44 transcript variant X19 XM_047434660.1:c.54_61= XM_047434660.1:c.58_61del
FBXO44 transcript variant X12 XM_047434647.1:c.54_61= XM_047434647.1:c.58_61del
FBXO44 transcript variant X10 XM_047434637.1:c.54_61= XM_047434637.1:c.58_61del
FBXO44 transcript variant X17 XM_047434659.1:c.54_61= XM_047434659.1:c.58_61del
FBXO44 transcript variant X14 XR_007064917.1:n.532_539= XR_007064917.1:n.532CACG[1]
FBXO44 transcript variant X9 XR_007064914.1:n.160_167= XR_007064914.1:n.160CACG[1]
FBXO44 transcript variant X20 XR_007064919.1:n.259_266= XR_007064919.1:n.259CACG[1]
FBXO44 transcript variant X5 XR_007064913.1:n.160_167= XR_007064913.1:n.160CACG[1]
FBXO44 transcript variant X18 XR_007064918.1:n.160_167= XR_007064918.1:n.160CACG[1]
F-box only protein 44 isoform 1 NP_149438.2:p.Phe18_Val21= NP_149438.2:p.His20fs
F-box only protein 44 isoform X1 XP_005263593.1:p.Phe18_Val21= XP_005263593.1:p.His20fs
F-box only protein 44 isoform X2 XP_006711108.1:p.Phe18_Val21= XP_006711108.1:p.His20fs
F-box only protein 44 isoform X1 XP_006711106.1:p.Phe18_Val21= XP_006711106.1:p.His20fs
F-box only protein 44 isoform 2 NP_904319.1:p.Phe18_Val21= NP_904319.1:p.His20fs
F-box only protein 44 isoform 2 NP_904320.1:p.Phe18_Val21= NP_904320.1:p.His20fs
F-box only protein 44 isoform X1 XP_016858331.1:p.Phe18_Val21= XP_016858331.1:p.His20fs
F-box only protein 44 isoform X3 XP_016858333.1:p.Phe18_Val21= XP_016858333.1:p.His20fs
F-box only protein 44 isoform X1 XP_011540737.1:p.Phe18_Val21= XP_011540737.1:p.His20fs
F-box only protein 44 isoform 1 NP_001014765.1:p.Phe18_Val21= NP_001014765.1:p.His20fs
F-box only protein 44 isoform 1 NP_001291720.1:p.Phe18_Val21= NP_001291720.1:p.His20fs
F-box only protein 44 isoform X1 XP_005263594.1:p.Phe18_Val21= XP_005263594.1:p.His20fs
F-box only protein 44 isoform 3 NP_001317284.1:p.Phe18_Val21= NP_001317284.1:p.His20fs
F-box only protein 44 isoform 2 NP_001291719.1:p.Phe18_Val21= NP_001291719.1:p.His20fs
F-box only protein 44 isoform X2 XP_016858332.1:p.Phe18_Val21= XP_016858332.1:p.His20fs
F-box only protein 44 isoform X2 XP_047290608.1:p.Phe18_Val21= XP_047290608.1:p.His20fs
F-box only protein 44 isoform X2 XP_047290591.1:p.Phe18_Val21= XP_047290591.1:p.His20fs
F-box only protein 44 isoform X1 XP_047290587.1:p.Phe18_Val21= XP_047290587.1:p.His20fs
F-box only protein 44 isoform X3 XP_047290616.1:p.Phe18_Val21= XP_047290616.1:p.His20fs
F-box only protein 44 isoform X2 XP_047290603.1:p.Phe18_Val21= XP_047290603.1:p.His20fs
F-box only protein 44 isoform X2 XP_047290593.1:p.Phe18_Val21= XP_047290593.1:p.His20fs
F-box only protein 44 isoform X3 XP_047290615.1:p.Phe18_Val21= XP_047290615.1:p.His20fs
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 TOPMED ss4439340423 Apr 25, 2021 (155)
2 TopMed NC_000001.11 - 11655889 Apr 25, 2021 (155)
3 ALFA NC_000001.11 - 11655889 Apr 25, 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
2946758, ss4439340423 NC_000001.11:11655888:CACG: NC_000001.11:11655888:CACGCACG:CACG (self)
4141504696 NC_000001.11:11655888:CACGCACG:CACG NC_000001.11:11655888:CACGCACG:CACG (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 rs1459379639

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