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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.

rs1490961542

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr3:37052519-37052525 (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
dupCTGA
Variation Type
Indel Insertion and Deletion
Frequency
dupCTGA=0.00000 (0/14050, ALFA)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
LRRFIP2 : 500B Downstream 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 TGACTGA=1.00000 TGACTGACTGA=0.00000 1.0 0.0 0.0 N/A
European Sub 9690 TGACTGA=1.0000 TGACTGACTGA=0.0000 1.0 0.0 0.0 N/A
African Sub 2898 TGACTGA=1.0000 TGACTGACTGA=0.0000 1.0 0.0 0.0 N/A
African Others Sub 114 TGACTGA=1.000 TGACTGACTGA=0.000 1.0 0.0 0.0 N/A
African American Sub 2784 TGACTGA=1.0000 TGACTGACTGA=0.0000 1.0 0.0 0.0 N/A
Asian Sub 112 TGACTGA=1.000 TGACTGACTGA=0.000 1.0 0.0 0.0 N/A
East Asian Sub 86 TGACTGA=1.00 TGACTGACTGA=0.00 1.0 0.0 0.0 N/A
Other Asian Sub 26 TGACTGA=1.00 TGACTGACTGA=0.00 1.0 0.0 0.0 N/A
Latin American 1 Sub 146 TGACTGA=1.000 TGACTGACTGA=0.000 1.0 0.0 0.0 N/A
Latin American 2 Sub 610 TGACTGA=1.000 TGACTGACTGA=0.000 1.0 0.0 0.0 N/A
South Asian Sub 98 TGACTGA=1.00 TGACTGACTGA=0.00 1.0 0.0 0.0 N/A
Other Sub 496 TGACTGA=1.000 TGACTGACTGA=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
Allele Frequency Aggregator Total Global 14050 TGACTGA=1.00000 dupCTGA=0.00000
Allele Frequency Aggregator European Sub 9690 TGACTGA=1.0000 dupCTGA=0.0000
Allele Frequency Aggregator African Sub 2898 TGACTGA=1.0000 dupCTGA=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 TGACTGA=1.000 dupCTGA=0.000
Allele Frequency Aggregator Other Sub 496 TGACTGA=1.000 dupCTGA=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 TGACTGA=1.000 dupCTGA=0.000
Allele Frequency Aggregator Asian Sub 112 TGACTGA=1.000 dupCTGA=0.000
Allele Frequency Aggregator South Asian Sub 98 TGACTGA=1.00 dupCTGA=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 3 NC_000003.12:g.37052522_37052525dup
GRCh37.p13 chr 3 NC_000003.11:g.37094013_37094016dup
MLH1 RefSeqGene (LRG_216) NG_007109.2:g.64173_64176dup
LRRFIP2 RefSeqGene NG_053016.1:g.129296_129299dup
Gene: LRRFIP2, LRR binding FLII interacting protein 2 (minus strand) : 500B Downstream Variant
Molecule type Change Amino acid[Codon] SO Term
LRRFIP2 transcript variant 3 NM_001134369.2:c. N/A Downstream Transcript Variant
LRRFIP2 transcript variant 4 NM_001282691.1:c. N/A Downstream Transcript Variant
LRRFIP2 transcript variant 5 NM_001348297.1:c. N/A Downstream Transcript Variant
LRRFIP2 transcript variant 6 NM_001348298.1:c. N/A Downstream Transcript Variant
LRRFIP2 transcript variant 7 NM_001348299.1:c. N/A Downstream Transcript Variant
LRRFIP2 transcript variant 8 NM_001348300.1:c. N/A Downstream Transcript Variant
LRRFIP2 transcript variant 9 NM_001348301.1:c. N/A Downstream Transcript Variant
LRRFIP2 transcript variant 10 NM_001348302.1:c. N/A Downstream Transcript Variant
LRRFIP2 transcript variant 11 NM_001348303.1:c. N/A Downstream Transcript Variant
LRRFIP2 transcript variant 12 NM_001348304.1:c. N/A Downstream Transcript Variant
LRRFIP2 transcript variant 13 NM_001348305.1:c. N/A Downstream Transcript Variant
LRRFIP2 transcript variant 14 NM_001348306.1:c. N/A Downstream Transcript Variant
LRRFIP2 transcript variant 15 NM_001348307.1:c. N/A Downstream Transcript Variant
LRRFIP2 transcript variant 16 NM_001348308.1:c. N/A Downstream Transcript Variant
LRRFIP2 transcript variant 17 NM_001348309.1:c. N/A Downstream Transcript Variant
LRRFIP2 transcript variant 18 NM_001348310.1:c. N/A Downstream Transcript Variant
LRRFIP2 transcript variant 19 NM_001348311.1:c. N/A Downstream Transcript Variant
LRRFIP2 transcript variant 1 NM_006309.4:c. N/A Downstream Transcript Variant
LRRFIP2 transcript variant 2 NM_017724.2:c. N/A Downstream Transcript Variant
LRRFIP2 transcript variant 20 NR_145514.2:n. N/A N/A
LRRFIP2 transcript variant X2 XM_005265539.3:c. N/A Downstream Transcript Variant
LRRFIP2 transcript variant X4 XM_005265540.2:c. N/A Downstream Transcript Variant
LRRFIP2 transcript variant X25 XM_005265551.2:c. N/A Downstream Transcript Variant
LRRFIP2 transcript variant X7 XM_006713385.2:c. N/A Downstream Transcript Variant
LRRFIP2 transcript variant X8 XM_006713387.2:c. N/A Downstream Transcript Variant
LRRFIP2 transcript variant X9 XM_006713388.2:c. N/A Downstream Transcript Variant
LRRFIP2 transcript variant X10 XM_006713389.2:c. N/A Downstream Transcript Variant
LRRFIP2 transcript variant X12 XM_006713390.2:c. N/A Downstream Transcript Variant
LRRFIP2 transcript variant X13 XM_006713392.2:c. N/A Downstream Transcript Variant
LRRFIP2 transcript variant X14 XM_006713393.2:c. N/A Downstream Transcript Variant
LRRFIP2 transcript variant X15 XM_006713395.2:c. N/A Downstream Transcript Variant
LRRFIP2 transcript variant X16 XM_006713396.2:c. N/A Downstream Transcript Variant
LRRFIP2 transcript variant X20 XM_006713397.2:c. N/A Downstream Transcript Variant
LRRFIP2 transcript variant X1 XM_011534217.2:c. N/A Downstream Transcript Variant
LRRFIP2 transcript variant X3 XM_011534218.2:c. N/A Downstream Transcript Variant
LRRFIP2 transcript variant X5 XM_011534219.2:c. N/A Downstream Transcript Variant
LRRFIP2 transcript variant X19 XM_011534222.2:c. N/A Downstream Transcript Variant
LRRFIP2 transcript variant X17 XM_017007467.2:c. N/A Downstream Transcript Variant
LRRFIP2 transcript variant X22 XM_017007469.2:c. N/A Downstream Transcript Variant
LRRFIP2 transcript variant X26 XM_017007471.2:c. N/A Downstream Transcript Variant
LRRFIP2 transcript variant X27 XM_017007472.2:c. N/A Downstream Transcript Variant
LRRFIP2 transcript variant X29 XM_017007473.2:c. N/A Downstream Transcript Variant
LRRFIP2 transcript variant X30 XM_017007476.2:c. N/A Downstream Transcript Variant
LRRFIP2 transcript variant X32 XM_017007479.2:c. N/A Downstream Transcript Variant
LRRFIP2 transcript variant X11 XM_024453820.2:c. N/A Downstream Transcript Variant
LRRFIP2 transcript variant X18 XM_024453821.2:c. N/A Downstream Transcript Variant
LRRFIP2 transcript variant X31 XM_024453824.2:c. N/A Downstream Transcript Variant
LRRFIP2 transcript variant X35 XM_024453826.2:c. N/A Downstream Transcript Variant
LRRFIP2 transcript variant X6 XM_047449201.1:c. N/A Downstream Transcript Variant
LRRFIP2 transcript variant X21 XM_047449202.1:c. N/A Downstream Transcript Variant
LRRFIP2 transcript variant X23 XM_047449203.1:c. N/A Downstream Transcript Variant
LRRFIP2 transcript variant X24 XM_047449204.1:c. N/A Downstream Transcript Variant
LRRFIP2 transcript variant X28 XM_047449205.1:c. N/A Downstream Transcript Variant
LRRFIP2 transcript variant X33 XM_047449206.1:c. N/A Downstream Transcript Variant
LRRFIP2 transcript variant X34 XM_047449207.1:c. N/A Downstream Transcript Variant
LRRFIP2 transcript variant X36 XM_047449208.1:c. N/A Downstream 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 TGACTGA= dupCTGA
GRCh38.p14 chr 3 NC_000003.12:g.37052519_37052525= NC_000003.12:g.37052522_37052525dup
GRCh37.p13 chr 3 NC_000003.11:g.37094010_37094016= NC_000003.11:g.37094013_37094016dup
MLH1 RefSeqGene (LRG_216) NG_007109.2:g.64170_64176= NG_007109.2:g.64173_64176dup
LRRFIP2 RefSeqGene NG_053016.1:g.129293_129299= NG_053016.1:g.129296_129299dup
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 Frequency submission
No Submitter Submission ID Date (Build)
1 ALFA NC_000003.12 - 37052519 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
8561675879 NC_000003.12:37052518:TGACTGA:TGAC…

NC_000003.12:37052518:TGACTGA:TGACTGACTGA

 NC_000003.12:37052518:TGACTGA:TGAC…

NC_000003.12:37052518:TGACTGA:TGACTGACTGA

 (self)
Removed from this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Destination RSIDs
248818706, ss3387645363 NC_000003.12:37052518::TGAC NC_000003.12:37052518:TGACTGA:TGAC…

NC_000003.12:37052518:TGACTGA:TGACTGACTGA
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 rs1490961542

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