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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.

rs1452494570

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr17:75896804-75896806 (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
delT
Variation Type
Indel Insertion and Deletion
Frequency
delT=0.000004 (1/264690, TOPMED)
delT=0.00000 (0/11862, ALFA)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
TRIM65 : Frameshift 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 TTT=1.00000 TT=0.00000 1.0 0.0 0.0 N/A
European Sub 7618 TTT=1.0000 TT=0.0000 1.0 0.0 0.0 N/A
African Sub 2816 TTT=1.0000 TT=0.0000 1.0 0.0 0.0 N/A
African Others Sub 108 TTT=1.000 TT=0.000 1.0 0.0 0.0 N/A
African American Sub 2708 TTT=1.0000 TT=0.0000 1.0 0.0 0.0 N/A
Asian Sub 108 TTT=1.000 TT=0.000 1.0 0.0 0.0 N/A
East Asian Sub 84 TTT=1.00 TT=0.00 1.0 0.0 0.0 N/A
Other Asian Sub 24 TTT=1.00 TT=0.00 1.0 0.0 0.0 N/A
Latin American 1 Sub 146 TTT=1.000 TT=0.000 1.0 0.0 0.0 N/A
Latin American 2 Sub 610 TTT=1.000 TT=0.000 1.0 0.0 0.0 N/A
South Asian Sub 94 TTT=1.00 TT=0.00 1.0 0.0 0.0 N/A
Other Sub 470 TTT=1.000 TT=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 TTT=0.999996 delT=0.000004
Allele Frequency Aggregator Total Global 11862 TTT=1.00000 delT=0.00000
Allele Frequency Aggregator European Sub 7618 TTT=1.0000 delT=0.0000
Allele Frequency Aggregator African Sub 2816 TTT=1.0000 delT=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 TTT=1.000 delT=0.000
Allele Frequency Aggregator Other Sub 470 TTT=1.000 delT=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 TTT=1.000 delT=0.000
Allele Frequency Aggregator Asian Sub 108 TTT=1.000 delT=0.000
Allele Frequency Aggregator South Asian Sub 94 TTT=1.00 delT=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 17 NC_000017.11:g.75896806del
GRCh37.p13 chr 17 NC_000017.10:g.73892887del
Gene: TRIM65, tripartite motif containing 65 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
TRIM65 transcript variant 1 NM_173547.4:c.134del K [AAG] > R [AG] Coding Sequence Variant
E3 ubiquitin-protein ligase TRIM65 isoform 1 NP_775818.2:p.Lys45fs K (Lys) > R (Arg) Frameshift Variant
TRIM65 transcript variant 2 NM_001256124.2:c.134del K [AAG] > R [AG] Coding Sequence Variant
E3 ubiquitin-protein ligase TRIM65 isoform 2 NP_001243053.1:p.Lys45fs K (Lys) > R (Arg) Frameshift Variant
TRIM65 transcript variant X1 XM_047435580.1:c.134del K [AAG] > R [AG] Coding Sequence Variant
E3 ubiquitin-protein ligase TRIM65 isoform X1 XP_047291536.1:p.Lys45fs K (Lys) > R (Arg) Frameshift Variant
TRIM65 transcript variant X2 XM_047435581.1:c.134del K [AAG] > R [AG] Coding Sequence Variant
E3 ubiquitin-protein ligase TRIM65 isoform X2 XP_047291537.1:p.Lys45fs K (Lys) > R (Arg) Frameshift Variant
TRIM65 transcript variant X3 XM_006721760.4:c.134del K [AAG] > R [AG] Coding Sequence Variant
E3 ubiquitin-protein ligase TRIM65 isoform X3 XP_006721823.1:p.Lys45fs K (Lys) > R (Arg) Frameshift Variant
TRIM65 transcript variant X4 XM_006721761.4:c.134del K [AAG] > R [AG] Coding Sequence Variant
E3 ubiquitin-protein ligase TRIM65 isoform X4 XP_006721824.1:p.Lys45fs K (Lys) > R (Arg) Frameshift Variant
TRIM65 transcript variant X5 XM_011524499.3:c.134del K [AAG] > R [AG] Coding Sequence Variant
E3 ubiquitin-protein ligase TRIM65 isoform X5 XP_011522801.1:p.Lys45fs K (Lys) > R (Arg) Frameshift Variant
TRIM65 transcript variant X6 XM_011524500.3:c.134del K [AAG] > R [AG] Coding Sequence Variant
E3 ubiquitin-protein ligase TRIM65 isoform X6 XP_011522802.1:p.Lys45fs K (Lys) > R (Arg) Frameshift Variant
TRIM65 transcript variant X7 XM_047435583.1:c.134del K [AAG] > R [AG] Coding Sequence Variant
E3 ubiquitin-protein ligase TRIM65 isoform X7 XP_047291539.1:p.Lys45fs K (Lys) > R (Arg) Frameshift Variant
TRIM65 transcript variant X8 XM_011524501.3:c.134del K [AAG] > R [AG] Coding Sequence Variant
E3 ubiquitin-protein ligase TRIM65 isoform X8 XP_011522803.1:p.Lys45fs K (Lys) > R (Arg) Frameshift Variant
TRIM65 transcript variant X9 XM_011524502.3:c.134del K [AAG] > R [AG] Coding Sequence Variant
E3 ubiquitin-protein ligase TRIM65 isoform X9 XP_011522804.1:p.Lys45fs K (Lys) > R (Arg) Frameshift Variant
TRIM65 transcript variant X10 XM_047435584.1:c.134del K [AAG] > R [AG] Coding Sequence Variant
E3 ubiquitin-protein ligase TRIM65 isoform X10 XP_047291540.1:p.Lys45fs K (Lys) > R (Arg) Frameshift Variant
TRIM65 transcript variant X11 XM_047435585.1:c.134del K [AAG] > R [AG] Coding Sequence Variant
E3 ubiquitin-protein ligase TRIM65 isoform X11 XP_047291541.1:p.Lys45fs K (Lys) > R (Arg) Frameshift Variant
TRIM65 transcript variant X12 XM_011524503.3:c.134del K [AAG] > R [AG] Coding Sequence Variant
E3 ubiquitin-protein ligase TRIM65 isoform X12 XP_011522805.1:p.Lys45fs K (Lys) > R (Arg) Frameshift Variant
TRIM65 transcript variant X14 XM_017024344.2:c.134del K [AAG] > R [AG] Coding Sequence Variant
E3 ubiquitin-protein ligase TRIM65 isoform X13 XP_016879833.1:p.Lys45fs K (Lys) > R (Arg) Frameshift Variant
TRIM65 transcript variant X13 XR_934419.3:n.148del 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 TTT= delT
GRCh38.p14 chr 17 NC_000017.11:g.75896804_75896806= NC_000017.11:g.75896806del
GRCh37.p13 chr 17 NC_000017.10:g.73892885_73892887= NC_000017.10:g.73892887del
TRIM65 transcript variant X3 XM_006721760.4:c.132_134= XM_006721760.4:c.134del
TRIM65 transcript variant X1 XM_006721760.3:c.132_134= XM_006721760.3:c.134del
TRIM65 transcript variant X1 XM_006721760.2:c.132_134= XM_006721760.2:c.134del
TRIM65 transcript variant X1 XM_006721760.1:c.132_134= XM_006721760.1:c.134del
TRIM65 transcript variant 1 NM_173547.4:c.132_134= NM_173547.4:c.134del
TRIM65 transcript variant 1 NM_173547.3:c.132_134= NM_173547.3:c.134del
TRIM65 transcript variant X4 XM_006721761.4:c.132_134= XM_006721761.4:c.134del
TRIM65 transcript variant X2 XM_006721761.3:c.132_134= XM_006721761.3:c.134del
TRIM65 transcript variant X2 XM_006721761.2:c.132_134= XM_006721761.2:c.134del
TRIM65 transcript variant X2 XM_006721761.1:c.132_134= XM_006721761.1:c.134del
TRIM65 transcript variant X12 XM_011524503.3:c.132_134= XM_011524503.3:c.134del
TRIM65 transcript variant X8 XM_011524503.2:c.132_134= XM_011524503.2:c.134del
TRIM65 transcript variant X7 XM_011524503.1:c.132_134= XM_011524503.1:c.134del
TRIM65 transcript variant X5 XM_011524499.3:c.132_134= XM_011524499.3:c.134del
TRIM65 transcript variant X3 XM_011524499.2:c.132_134= XM_011524499.2:c.134del
TRIM65 transcript variant X3 XM_011524499.1:c.132_134= XM_011524499.1:c.134del
TRIM65 transcript variant X8 XM_011524501.3:c.132_134= XM_011524501.3:c.134del
TRIM65 transcript variant X5 XM_011524501.2:c.132_134= XM_011524501.2:c.134del
TRIM65 transcript variant X5 XM_011524501.1:c.132_134= XM_011524501.1:c.134del
TRIM65 transcript variant X13 XR_934419.3:n.146_148= XR_934419.3:n.148del
TRIM65 transcript variant X9 XR_934419.2:n.203_205= XR_934419.2:n.205del
TRIM65 transcript variant X8 XR_934419.1:n.192_194= XR_934419.1:n.194del
TRIM65 transcript variant X6 XM_011524500.3:c.132_134= XM_011524500.3:c.134del
TRIM65 transcript variant X4 XM_011524500.2:c.132_134= XM_011524500.2:c.134del
TRIM65 transcript variant X4 XM_011524500.1:c.132_134= XM_011524500.1:c.134del
TRIM65 transcript variant X9 XM_011524502.3:c.132_134= XM_011524502.3:c.134del
TRIM65 transcript variant X6 XM_011524502.2:c.132_134= XM_011524502.2:c.134del
TRIM65 transcript variant X6 XM_011524502.1:c.132_134= XM_011524502.1:c.134del
TRIM65 transcript variant 2 NM_001256124.2:c.132_134= NM_001256124.2:c.134del
TRIM65 transcript variant 2 NM_001256124.1:c.132_134= NM_001256124.1:c.134del
TRIM65 transcript variant X14 XM_017024344.2:c.132_134= XM_017024344.2:c.134del
TRIM65 transcript variant X10 XM_017024344.1:c.132_134= XM_017024344.1:c.134del
TRIM65 transcript variant X1 XM_047435580.1:c.132_134= XM_047435580.1:c.134del
TRIM65 transcript variant X2 XM_047435581.1:c.132_134= XM_047435581.1:c.134del
TRIM65 transcript variant X7 XM_047435583.1:c.132_134= XM_047435583.1:c.134del
TRIM65 transcript variant X10 XM_047435584.1:c.132_134= XM_047435584.1:c.134del
TRIM65 transcript variant X11 XM_047435585.1:c.132_134= XM_047435585.1:c.134del
E3 ubiquitin-protein ligase TRIM65 isoform X3 XP_006721823.1:p.Gly44_Lys45= XP_006721823.1:p.Lys45fs
E3 ubiquitin-protein ligase TRIM65 isoform 1 NP_775818.2:p.Gly44_Lys45= NP_775818.2:p.Lys45fs
E3 ubiquitin-protein ligase TRIM65 isoform X4 XP_006721824.1:p.Gly44_Lys45= XP_006721824.1:p.Lys45fs
E3 ubiquitin-protein ligase TRIM65 isoform X12 XP_011522805.1:p.Gly44_Lys45= XP_011522805.1:p.Lys45fs
E3 ubiquitin-protein ligase TRIM65 isoform X5 XP_011522801.1:p.Gly44_Lys45= XP_011522801.1:p.Lys45fs
E3 ubiquitin-protein ligase TRIM65 isoform X8 XP_011522803.1:p.Gly44_Lys45= XP_011522803.1:p.Lys45fs
E3 ubiquitin-protein ligase TRIM65 isoform X6 XP_011522802.1:p.Gly44_Lys45= XP_011522802.1:p.Lys45fs
E3 ubiquitin-protein ligase TRIM65 isoform X9 XP_011522804.1:p.Gly44_Lys45= XP_011522804.1:p.Lys45fs
E3 ubiquitin-protein ligase TRIM65 isoform 2 NP_001243053.1:p.Gly44_Lys45= NP_001243053.1:p.Lys45fs
E3 ubiquitin-protein ligase TRIM65 isoform X13 XP_016879833.1:p.Gly44_Lys45= XP_016879833.1:p.Lys45fs
E3 ubiquitin-protein ligase TRIM65 isoform X1 XP_047291536.1:p.Gly44_Lys45= XP_047291536.1:p.Lys45fs
E3 ubiquitin-protein ligase TRIM65 isoform X2 XP_047291537.1:p.Gly44_Lys45= XP_047291537.1:p.Lys45fs
E3 ubiquitin-protein ligase TRIM65 isoform X7 XP_047291539.1:p.Gly44_Lys45= XP_047291539.1:p.Lys45fs
E3 ubiquitin-protein ligase TRIM65 isoform X10 XP_047291540.1:p.Gly44_Lys45= XP_047291540.1:p.Lys45fs
E3 ubiquitin-protein ligase TRIM65 isoform X11 XP_047291541.1:p.Gly44_Lys45= XP_047291541.1:p.Lys45fs
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 ss5044041746 Apr 26, 2021 (155)
2 TopMed NC_000017.11 - 75896804 Apr 26, 2021 (155)
3 ALFA NC_000017.11 - 75896804 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
259587408, ss5044041746 NC_000017.11:75896803:T: NC_000017.11:75896803:TTT:TT (self)
687125177 NC_000017.11:75896803:TTT:TT NC_000017.11:75896803:TTT:TT (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 rs1452494570

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