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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.

rs1473321595

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr13:114281944 (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
C>G / C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.00004 (1/27806, 14KJPN)
G=0.00006 (1/16504, 8.3KJPN)
T=0.00000 (0/11862, ALFA)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
UPF3A : Non Coding Transcript Variant
LOC105370384 : 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 C=1.00000 T=0.00000 1.0 0.0 0.0 N/A
European Sub 7618 C=1.0000 T=0.0000 1.0 0.0 0.0 N/A
African Sub 2816 C=1.0000 T=0.0000 1.0 0.0 0.0 N/A
African Others Sub 108 C=1.000 T=0.000 1.0 0.0 0.0 N/A
African American Sub 2708 C=1.0000 T=0.0000 1.0 0.0 0.0 N/A
Asian Sub 108 C=1.000 T=0.000 1.0 0.0 0.0 N/A
East Asian Sub 84 C=1.00 T=0.00 1.0 0.0 0.0 N/A
Other Asian Sub 24 C=1.00 T=0.00 1.0 0.0 0.0 N/A
Latin American 1 Sub 146 C=1.000 T=0.000 1.0 0.0 0.0 N/A
Latin American 2 Sub 610 C=1.000 T=0.000 1.0 0.0 0.0 N/A
South Asian Sub 94 C=1.00 T=0.00 1.0 0.0 0.0 N/A
Other Sub 470 C=1.000 T=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
14KJPN JAPANESE Study-wide 27806 C=0.99996 G=0.00004
8.3KJPN JAPANESE Study-wide 16504 C=0.99994 G=0.00006
Allele Frequency Aggregator Total Global 11862 C=1.00000 T=0.00000
Allele Frequency Aggregator European Sub 7618 C=1.0000 T=0.0000
Allele Frequency Aggregator African Sub 2816 C=1.0000 T=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 C=1.000 T=0.000
Allele Frequency Aggregator Other Sub 470 C=1.000 T=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 C=1.000 T=0.000
Allele Frequency Aggregator Asian Sub 108 C=1.000 T=0.000
Allele Frequency Aggregator South Asian Sub 94 C=1.00 T=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 13 NC_000013.11:g.114281944C>G
GRCh38.p14 chr 13 NC_000013.11:g.114281944C>T
GRCh37.p13 chr 13 NC_000013.10:g.115047419C>G
GRCh37.p13 chr 13 NC_000013.10:g.115047419C>T
UPF3A RefSeqGene NG_029528.1:g.5361C>G
UPF3A RefSeqGene NG_029528.1:g.5361C>T
Gene: UPF3A, UPF3A regulator of nonsense mediated mRNA decay (plus strand)
Molecule type Change Amino acid[Codon] SO Term
UPF3A transcript variant 3 NM_001353644.2:c.-183+98C…

NM_001353644.2:c.-183+98C>G

 		N/A Intron Variant
UPF3A transcript variant 10 NM_001353651.2:c.208-77C>G N/A Intron Variant
UPF3A transcript variant 11 NM_001353652.2:c.208-77C>G N/A Intron Variant
UPF3A transcript variant 1 NM_023011.4:c.208-77C>G N/A Intron Variant
UPF3A transcript variant 2 NM_080687.3:c.208-77C>G N/A Intron Variant
UPF3A transcript variant 4 NM_001353645.1:c.-738= N/A 5 Prime UTR Variant
UPF3A transcript variant 8 NM_001353649.1:c.-374= N/A 5 Prime UTR Variant
UPF3A transcript variant 5 NM_001353646.1:c.-374= N/A 5 Prime UTR Variant
UPF3A transcript variant 9 NM_001353650.1:c.-738= N/A 5 Prime UTR Variant
UPF3A transcript variant 6 NM_001353647.1:c.-473= N/A 5 Prime UTR Variant
UPF3A transcript variant 7 NM_001353648.2:c. N/A Genic Upstream Transcript Variant
UPF3A transcript variant 18 NR_148488.1:n.34C>G N/A Non Coding Transcript Variant
UPF3A transcript variant 18 NR_148488.1:n.34C>T N/A Non Coding Transcript Variant
UPF3A transcript variant 23 NR_148493.1:n.34C>G N/A Non Coding Transcript Variant
UPF3A transcript variant 23 NR_148493.1:n.34C>T N/A Non Coding Transcript Variant
UPF3A transcript variant 21 NR_148491.1:n.34C>G N/A Non Coding Transcript Variant
UPF3A transcript variant 21 NR_148491.1:n.34C>T N/A Non Coding Transcript Variant
UPF3A transcript variant 26 NR_148496.1:n.34C>G N/A Non Coding Transcript Variant
UPF3A transcript variant 26 NR_148496.1:n.34C>T N/A Non Coding Transcript Variant
UPF3A transcript variant 24 NR_148494.1:n.34C>G N/A Non Coding Transcript Variant
UPF3A transcript variant 24 NR_148494.1:n.34C>T N/A Non Coding Transcript Variant
UPF3A transcript variant 25 NR_148495.1:n.34C>G N/A Non Coding Transcript Variant
UPF3A transcript variant 25 NR_148495.1:n.34C>T N/A Non Coding Transcript Variant
UPF3A transcript variant 22 NR_148492.1:n.34C>G N/A Non Coding Transcript Variant
UPF3A transcript variant 22 NR_148492.1:n.34C>T N/A Non Coding Transcript Variant
UPF3A transcript variant 17 NR_148487.1:n.34C>G N/A Non Coding Transcript Variant
UPF3A transcript variant 17 NR_148487.1:n.34C>T N/A Non Coding Transcript Variant
UPF3A transcript variant 20 NR_148490.1:n.34C>G N/A Non Coding Transcript Variant
UPF3A transcript variant 20 NR_148490.1:n.34C>T N/A Non Coding Transcript Variant
UPF3A transcript variant 19 NR_148489.1:n.34C>G N/A Non Coding Transcript Variant
UPF3A transcript variant 19 NR_148489.1:n.34C>T N/A Non Coding Transcript Variant
UPF3A transcript variant 16 NR_148486.1:n.34C>G N/A Non Coding Transcript Variant
UPF3A transcript variant 16 NR_148486.1:n.34C>T N/A Non Coding Transcript Variant
UPF3A transcript variant 12 NR_148482.2:n. N/A Intron Variant
UPF3A transcript variant 13 NR_148483.2:n. N/A Intron Variant
UPF3A transcript variant 14 NR_148484.2:n. N/A Intron Variant
UPF3A transcript variant 15 NR_148485.2:n. N/A Intron Variant
UPF3A transcript variant X1 XM_011534844.2:c.208-77C>G N/A Intron Variant
UPF3A transcript variant X3 XM_011534846.2:c.208-77C>G N/A Intron Variant
UPF3A transcript variant X7 XM_024449402.2:c.208-77C>G N/A Intron Variant
UPF3A transcript variant X9 XM_024449403.2:c.208-77C>G N/A Intron Variant
UPF3A transcript variant X4 XM_047430546.1:c.208-77C>G N/A Intron Variant
UPF3A transcript variant X5 XM_047430547.1:c.208-77C>G N/A Intron Variant
UPF3A transcript variant X8 XM_047430549.1:c.208-77C>G 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
Gene: LOC105370384, uncharacterized LOC105370384 (minus strand) : 2KB Upstream 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
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 C= G T
GRCh38.p14 chr 13 NC_000013.11:g.114281944= NC_000013.11:g.114281944C>G NC_000013.11:g.114281944C>T
GRCh37.p13 chr 13 NC_000013.10:g.115047419= NC_000013.10:g.115047419C>G NC_000013.10:g.115047419C>T
UPF3A RefSeqGene NG_029528.1:g.5361= NG_029528.1:g.5361C>G NG_029528.1:g.5361C>T
UPF3A transcript variant 4 NM_001353645.1:c.-738= NM_001353645.1:c.-738C>G NM_001353645.1:c.-738C>T
UPF3A transcript variant 9 NM_001353650.1:c.-738= NM_001353650.1:c.-738C>G NM_001353650.1:c.-738C>T
UPF3A transcript variant 6 NM_001353647.1:c.-473= NM_001353647.1:c.-473C>G NM_001353647.1:c.-473C>T
UPF3A transcript variant 21 NR_148491.1:n.34= NR_148491.1:n.34C>G NR_148491.1:n.34C>T
UPF3A transcript variant 5 NM_001353646.1:c.-374= NM_001353646.1:c.-374C>G NM_001353646.1:c.-374C>T
UPF3A transcript variant 8 NM_001353649.1:c.-374= NM_001353649.1:c.-374C>G NM_001353649.1:c.-374C>T
UPF3A transcript variant 16 NR_148486.1:n.34= NR_148486.1:n.34C>G NR_148486.1:n.34C>T
UPF3A transcript variant 17 NR_148487.1:n.34= NR_148487.1:n.34C>G NR_148487.1:n.34C>T
UPF3A transcript variant 22 NR_148492.1:n.34= NR_148492.1:n.34C>G NR_148492.1:n.34C>T
UPF3A transcript variant 19 NR_148489.1:n.34= NR_148489.1:n.34C>G NR_148489.1:n.34C>T
UPF3A transcript variant 23 NR_148493.1:n.34= NR_148493.1:n.34C>G NR_148493.1:n.34C>T
UPF3A transcript variant 26 NR_148496.1:n.34= NR_148496.1:n.34C>G NR_148496.1:n.34C>T
UPF3A transcript variant 18 NR_148488.1:n.34= NR_148488.1:n.34C>G NR_148488.1:n.34C>T
UPF3A transcript variant 20 NR_148490.1:n.34= NR_148490.1:n.34C>G NR_148490.1:n.34C>T
UPF3A transcript variant 24 NR_148494.1:n.34= NR_148494.1:n.34C>G NR_148494.1:n.34C>T
UPF3A transcript variant 25 NR_148495.1:n.34= NR_148495.1:n.34C>G NR_148495.1:n.34C>T
UPF3A transcript variant 3 NM_001353644.2:c.-183+98= NM_001353644.2:c.-183+98C>G NM_001353644.2:c.-183+98C>T
UPF3A transcript variant 10 NM_001353651.2:c.208-77= NM_001353651.2:c.208-77C>G NM_001353651.2:c.208-77C>T
UPF3A transcript variant 11 NM_001353652.2:c.208-77= NM_001353652.2:c.208-77C>G NM_001353652.2:c.208-77C>T
UPF3A transcript variant 1 NM_023011.3:c.208-77= NM_023011.3:c.208-77C>G NM_023011.3:c.208-77C>T
UPF3A transcript variant 1 NM_023011.4:c.208-77= NM_023011.4:c.208-77C>G NM_023011.4:c.208-77C>T
UPF3A transcript variant 2 NM_080687.2:c.208-77= NM_080687.2:c.208-77C>G NM_080687.2:c.208-77C>T
UPF3A transcript variant 2 NM_080687.3:c.208-77= NM_080687.3:c.208-77C>G NM_080687.3:c.208-77C>T
UPF3A transcript variant X1 XM_005266198.1:c.208-77= XM_005266198.1:c.208-77C>G XM_005266198.1:c.208-77C>T
UPF3A transcript variant X5 XM_005266200.1:c.208-77= XM_005266200.1:c.208-77C>G XM_005266200.1:c.208-77C>T
UPF3A transcript variant X1 XM_011534844.2:c.208-77= XM_011534844.2:c.208-77C>G XM_011534844.2:c.208-77C>T
UPF3A transcript variant X3 XM_011534846.2:c.208-77= XM_011534846.2:c.208-77C>G XM_011534846.2:c.208-77C>T
UPF3A transcript variant X7 XM_024449402.2:c.208-77= XM_024449402.2:c.208-77C>G XM_024449402.2:c.208-77C>T
UPF3A transcript variant X9 XM_024449403.2:c.208-77= XM_024449403.2:c.208-77C>G XM_024449403.2:c.208-77C>T
UPF3A transcript variant X4 XM_047430546.1:c.208-77= XM_047430546.1:c.208-77C>G XM_047430546.1:c.208-77C>T
UPF3A transcript variant X5 XM_047430547.1:c.208-77= XM_047430547.1:c.208-77C>G XM_047430547.1:c.208-77C>T
UPF3A transcript variant X8 XM_047430549.1:c.208-77= XM_047430549.1:c.208-77C>G XM_047430549.1:c.208-77C>T
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#.

2 SubSNP, 3 Frequency submissions
No Submitter Submission ID Date (Build)
1 TOMMO_GENOMICS ss5212083466 Apr 27, 2021 (155)
2 TOMMO_GENOMICS ss5764547638 Oct 16, 2022 (156)
3 8.3KJPN NC_000013.10 - 115047419 Apr 27, 2021 (155)
4 14KJPN NC_000013.11 - 114281944 Oct 16, 2022 (156)
5 ALFA NC_000013.11 - 114281944 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
70052773, ss5212083466 NC_000013.10:115047418:C:G NC_000013.11:114281943:C:G (self)
98384742, ss5764547638 NC_000013.11:114281943:C:G NC_000013.11:114281943:C:G
4400445456 NC_000013.11:114281943:C:T NC_000013.11:114281943:C:T (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 rs1473321595

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