dbSNP Short Genetic Variations
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.
rs1477290558
Current Build 156
Released September 21, 2022
- Organism
- Homo sapiens
- Position
-
chr13:114282117 (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
- G>A
- Variation Type
- SNV Single Nucleotide Variation
- Frequency
-
None
- Clinical Significance
- Not Reported in ClinVar
- Gene : Consequence
-
UPF3A : Missense VariantLOC105370384 : 2KB Upstream Variant
- Publications
- 0 citations
- Genomic View
- See rs on genome
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").
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.
| Sequence name | Change |
|---|---|
| GRCh38.p14 chr 13 | NC_000013.11:g.114282117G>A |
| GRCh37.p13 chr 13 | NC_000013.10:g.115047592G>A |
| UPF3A RefSeqGene | NG_029528.1:g.5534G>A |
| Molecule type | Change | Amino acid[Codon] | SO Term |
|---|---|---|---|
| UPF3A transcript variant 3 |
NM_001353644.2:c.-183+271… NM_001353644.2:c.-183+271G>A |
N/A | Intron Variant |
| UPF3A transcript variant 4 | NM_001353645.1:c.-565= | N/A | 5 Prime UTR Variant |
| UPF3A transcript variant 8 | NM_001353649.1:c.-201= | N/A | 5 Prime UTR Variant |
| UPF3A transcript variant 5 | NM_001353646.1:c.-201= | N/A | 5 Prime UTR Variant |
| UPF3A transcript variant 9 | NM_001353650.1:c.-565= | N/A | 5 Prime UTR Variant |
| UPF3A transcript variant 6 | NM_001353647.1:c.-300= | N/A | 5 Prime UTR Variant |
| UPF3A transcript variant 7 | NM_001353648.2:c. | N/A | Genic Upstream Transcript Variant |
| UPF3A transcript variant 1 | NM_023011.4:c.304G>A | A [GCC] > T [ACC] | Coding Sequence Variant |
| regulator of nonsense transcripts 3A isoform hUpf3p | NP_075387.1:p.Ala102Thr | A (Ala) > T (Thr) | Missense Variant |
| UPF3A transcript variant 10 | NM_001353651.2:c.304G>A | A [GCC] > T [ACC] | Coding Sequence Variant |
| regulator of nonsense transcripts 3A isoform e | NP_001340580.1:p.Ala102Thr | A (Ala) > T (Thr) | Missense Variant |
| UPF3A transcript variant 2 | NM_080687.3:c.304G>A | A [GCC] > T [ACC] | Coding Sequence Variant |
| regulator of nonsense transcripts 3A isoform hUpf3pdelta | NP_542418.1:p.Ala102Thr | A (Ala) > T (Thr) | Missense Variant |
| UPF3A transcript variant 11 | NM_001353652.2:c.304G>A | A [GCC] > T [ACC] | Coding Sequence Variant |
| regulator of nonsense transcripts 3A isoform f | NP_001340581.1:p.Ala102Thr | A (Ala) > T (Thr) | Missense Variant |
| UPF3A transcript variant 18 | NR_148488.1:n.207G>A | N/A | Non Coding Transcript Variant |
| UPF3A transcript variant 23 | NR_148493.1:n.207G>A | N/A | Non Coding Transcript Variant |
| UPF3A transcript variant 21 | NR_148491.1:n.207G>A | N/A | Non Coding Transcript Variant |
| UPF3A transcript variant 26 | NR_148496.1:n.207G>A | N/A | Non Coding Transcript Variant |
| UPF3A transcript variant 24 | NR_148494.1:n.207G>A | N/A | Non Coding Transcript Variant |
| UPF3A transcript variant 25 | NR_148495.1:n.207G>A | N/A | Non Coding Transcript Variant |
| UPF3A transcript variant 22 | NR_148492.1:n.207G>A | N/A | Non Coding Transcript Variant |
| UPF3A transcript variant 17 | NR_148487.1:n.207G>A | N/A | Non Coding Transcript Variant |
| UPF3A transcript variant 20 | NR_148490.1:n.207G>A | N/A | Non Coding Transcript Variant |
| UPF3A transcript variant 19 | NR_148489.1:n.207G>A | N/A | Non Coding Transcript Variant |
| UPF3A transcript variant 16 | NR_148486.1:n.207G>A | N/A | Non Coding Transcript Variant |
| UPF3A transcript variant 13 | NR_148483.2:n.343G>A | N/A | Non Coding Transcript Variant |
| UPF3A transcript variant 12 | NR_148482.2:n.343G>A | N/A | Non Coding Transcript Variant |
| UPF3A transcript variant 15 | NR_148485.2:n.343G>A | N/A | Non Coding Transcript Variant |
| UPF3A transcript variant 14 | NR_148484.2:n. | N/A | Intron Variant |
| UPF3A transcript variant X2 | XM_011534845.3:c. | N/A | Genic Upstream Transcript Variant |
| UPF3A transcript variant X10 | XM_024449401.2:c. | N/A | Genic Upstream Transcript Variant |
| UPF3A transcript variant X6 | XM_047430548.1:c. | N/A | Genic Upstream Transcript Variant |
| UPF3A transcript variant X1 | XM_011534844.2:c.304G>A | A [GCC] > T [ACC] | Coding Sequence Variant |
| regulator of nonsense transcripts 3A isoform X1 | XP_011533146.1:p.Ala102Thr | A (Ala) > T (Thr) | Missense Variant |
| UPF3A transcript variant X3 | XM_011534846.2:c.304G>A | A [GCC] > T [ACC] | Coding Sequence Variant |
| regulator of nonsense transcripts 3A isoform X3 | XP_011533148.1:p.Ala102Thr | A (Ala) > T (Thr) | Missense Variant |
| UPF3A transcript variant X4 | XM_047430546.1:c.304G>A | A [GCC] > T [ACC] | Coding Sequence Variant |
| regulator of nonsense transcripts 3A isoform X4 | XP_047286502.1:p.Ala102Thr | A (Ala) > T (Thr) | Missense Variant |
| UPF3A transcript variant X5 | XM_047430547.1:c.304G>A | A [GCC] > T [ACC] | Coding Sequence Variant |
| regulator of nonsense transcripts 3A isoform X5 | XP_047286503.1:p.Ala102Thr | A (Ala) > T (Thr) | Missense Variant |
| UPF3A transcript variant X7 | XM_024449402.2:c.304G>A | A [GCC] > T [ACC] | Coding Sequence Variant |
| regulator of nonsense transcripts 3A isoform X7 | XP_024305170.1:p.Ala102Thr | A (Ala) > T (Thr) | Missense Variant |
| UPF3A transcript variant X8 | XM_047430549.1:c.304G>A | A [GCC] > T [ACC] | Coding Sequence Variant |
| regulator of nonsense transcripts 3A isoform X8 | XP_047286505.1:p.Ala102Thr | A (Ala) > T (Thr) | Missense Variant |
| UPF3A transcript variant X9 | XM_024449403.2:c.304G>A | A [GCC] > T [ACC] | Coding Sequence Variant |
| regulator of nonsense transcripts 3A isoform X9 | XP_024305171.1:p.Ala102Thr | A (Ala) > T (Thr) | Missense Variant |
| Molecule type | Change | Amino acid[Codon] | SO Term |
|---|---|---|---|
| LOC105370384 transcript variant X1 | XR_001750056.2:n. | N/A | Upstream Transcript Variant |
| LOC105370384 transcript variant X4 | XR_001750057.2:n. | N/A | Upstream Transcript Variant |
| LOC105370384 transcript variant X5 | XR_001750058.2:n. | N/A | Upstream Transcript Variant |
| LOC105370384 transcript variant X7 | XR_001750059.2:n. | N/A | Upstream Transcript Variant |
| LOC105370384 transcript variant X2 | XR_007063885.1:n. | N/A | Upstream Transcript Variant |
| LOC105370384 transcript variant X3 | XR_007063886.1:n. | N/A | Upstream Transcript Variant |
| LOC105370384 transcript variant X6 | XR_007063887.1:n. | N/A | Upstream Transcript Variant |
| LOC105370384 transcript variant X8 | XR_007063888.1:n. | N/A | Upstream Transcript Variant |
| LOC105370384 transcript variant X9 | XR_007063889.1:n. | N/A | Upstream Transcript Variant |
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.
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 | G= | A |
|---|---|---|
| GRCh38.p14 chr 13 | NC_000013.11:g.114282117= | NC_000013.11:g.114282117G>A |
| GRCh37.p13 chr 13 | NC_000013.10:g.115047592= | NC_000013.10:g.115047592G>A |
| UPF3A RefSeqGene | NG_029528.1:g.5534= | NG_029528.1:g.5534G>A |
| UPF3A transcript variant 1 | NM_023011.4:c.304= | NM_023011.4:c.304G>A |
| UPF3A transcript variant 1 | NM_023011.3:c.304= | NM_023011.3:c.304G>A |
| UPF3A transcript variant 2 | NM_080687.3:c.304= | NM_080687.3:c.304G>A |
| UPF3A transcript variant 2 | NM_080687.2:c.304= | NM_080687.2:c.304G>A |
| UPF3A transcript variant 12 | NR_148482.2:n.343= | NR_148482.2:n.343G>A |
| UPF3A transcript variant 12 | NR_148482.1:n.360= | NR_148482.1:n.360G>A |
| UPF3A transcript variant 15 | NR_148485.2:n.343= | NR_148485.2:n.343G>A |
| UPF3A transcript variant 15 | NR_148485.1:n.360= | NR_148485.1:n.360G>A |
| UPF3A transcript variant 11 | NM_001353652.2:c.304= | NM_001353652.2:c.304G>A |
| UPF3A transcript variant 11 | NM_001353652.1:c.304= | NM_001353652.1:c.304G>A |
| UPF3A transcript variant 13 | NR_148483.2:n.343= | NR_148483.2:n.343G>A |
| UPF3A transcript variant 13 | NR_148483.1:n.360= | NR_148483.1:n.360G>A |
| UPF3A transcript variant 10 | NM_001353651.2:c.304= | NM_001353651.2:c.304G>A |
| UPF3A transcript variant 10 | NM_001353651.1:c.304= | NM_001353651.1:c.304G>A |
| UPF3A transcript variant 4 | NM_001353645.1:c.-565= | NM_001353645.1:c.-565G>A |
| UPF3A transcript variant 9 | NM_001353650.1:c.-565= | NM_001353650.1:c.-565G>A |
| UPF3A transcript variant 6 | NM_001353647.1:c.-300= | NM_001353647.1:c.-300G>A |
| UPF3A transcript variant 21 | NR_148491.1:n.207= | NR_148491.1:n.207G>A |
| UPF3A transcript variant 5 | NM_001353646.1:c.-201= | NM_001353646.1:c.-201G>A |
| UPF3A transcript variant 8 | NM_001353649.1:c.-201= | NM_001353649.1:c.-201G>A |
| UPF3A transcript variant 16 | NR_148486.1:n.207= | NR_148486.1:n.207G>A |
| UPF3A transcript variant 17 | NR_148487.1:n.207= | NR_148487.1:n.207G>A |
| UPF3A transcript variant 22 | NR_148492.1:n.207= | NR_148492.1:n.207G>A |
| UPF3A transcript variant 19 | NR_148489.1:n.207= | NR_148489.1:n.207G>A |
| UPF3A transcript variant 23 | NR_148493.1:n.207= | NR_148493.1:n.207G>A |
| UPF3A transcript variant 26 | NR_148496.1:n.207= | NR_148496.1:n.207G>A |
| UPF3A transcript variant 18 | NR_148488.1:n.207= | NR_148488.1:n.207G>A |
| UPF3A transcript variant 20 | NR_148490.1:n.207= | NR_148490.1:n.207G>A |
| UPF3A transcript variant 24 | NR_148494.1:n.207= | NR_148494.1:n.207G>A |
| UPF3A transcript variant 25 | NR_148495.1:n.207= | NR_148495.1:n.207G>A |
| UPF3A transcript variant X1 | XM_011534844.2:c.304= | XM_011534844.2:c.304G>A |
| UPF3A transcript variant X1 | XM_011534844.1:c.304= | XM_011534844.1:c.304G>A |
| UPF3A transcript variant X3 | XM_011534846.2:c.304= | XM_011534846.2:c.304G>A |
| UPF3A transcript variant X5 | XM_011534846.1:c.304= | XM_011534846.1:c.304G>A |
| UPF3A transcript variant X7 | XM_024449402.2:c.304= | XM_024449402.2:c.304G>A |
| UPF3A transcript variant X15 | XM_024449402.1:c.304= | XM_024449402.1:c.304G>A |
| UPF3A transcript variant X9 | XM_024449403.2:c.304= | XM_024449403.2:c.304G>A |
| UPF3A transcript variant X18 | XM_024449403.1:c.304= | XM_024449403.1:c.304G>A |
| UPF3A transcript variant X4 | XM_047430546.1:c.304= | XM_047430546.1:c.304G>A |
| UPF3A transcript variant X5 | XM_047430547.1:c.304= | XM_047430547.1:c.304G>A |
| UPF3A transcript variant X8 | XM_047430549.1:c.304= | XM_047430549.1:c.304G>A |
| regulator of nonsense transcripts 3A isoform hUpf3p | NP_075387.1:p.Ala102= | NP_075387.1:p.Ala102Thr |
| regulator of nonsense transcripts 3A isoform hUpf3pdelta | NP_542418.1:p.Ala102= | NP_542418.1:p.Ala102Thr |
| regulator of nonsense transcripts 3A isoform f | NP_001340581.1:p.Ala102= | NP_001340581.1:p.Ala102Thr |
| regulator of nonsense transcripts 3A isoform e | NP_001340580.1:p.Ala102= | NP_001340580.1:p.Ala102Thr |
| regulator of nonsense transcripts 3A isoform X1 | XP_011533146.1:p.Ala102= | XP_011533146.1:p.Ala102Thr |
| regulator of nonsense transcripts 3A isoform X3 | XP_011533148.1:p.Ala102= | XP_011533148.1:p.Ala102Thr |
| regulator of nonsense transcripts 3A isoform X7 | XP_024305170.1:p.Ala102= | XP_024305170.1:p.Ala102Thr |
| regulator of nonsense transcripts 3A isoform X9 | XP_024305171.1:p.Ala102= | XP_024305171.1:p.Ala102Thr |
| regulator of nonsense transcripts 3A isoform X4 | XP_047286502.1:p.Ala102= | XP_047286502.1:p.Ala102Thr |
| regulator of nonsense transcripts 3A isoform X5 | XP_047286503.1:p.Ala102= | XP_047286503.1:p.Ala102Thr |
| regulator of nonsense transcripts 3A isoform X8 | XP_047286505.1:p.Ala102= | XP_047286505.1:p.Ala102Thr |
| UPF3A transcript variant 3 | NM_001353644.2:c.-183+271= | NM_001353644.2:c.-183+271G>A |
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#.
| No | Submitter | Submission ID | Date (Build) |
|---|---|---|---|
| 1 | GNOMAD | ss2740541036 | Nov 08, 2017 (151) |
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).
Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.
No publications for rs1477290558
The Flanks tab provides retrieving flanking sequences of a SNP on all molecules that have placements.
Genomic regions, transcripts, and products
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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.
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.