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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.

rs758199547

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr11:47235304 (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=0.000004 (1/264690, TOPMED)
G=0.000007 (1/140280, GnomAD)
T=0.000008 (1/121392, ExAC) (+ 2 more)
G=0.00000 (0/10680, ALFA)
T=0.0003 (1/2922, KOREAN)
Clinical Significance
Reported in ClinVar
Gene : Consequence
DDB2 : Synonymous 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: 20230706150541
Population Group Sample Size Ref Allele Alt Allele
Total Global 10680 C=1.00000 G=0.00000
European Sub 6962 C=1.0000 G=0.0000
African Sub 2294 C=1.0000 G=0.0000
African Others Sub 84 C=1.00 G=0.00
African American Sub 2210 C=1.0000 G=0.0000
Asian Sub 108 C=1.000 G=0.000
East Asian Sub 84 C=1.00 G=0.00
Other Asian Sub 24 C=1.00 G=0.00
Latin American 1 Sub 146 C=1.000 G=0.000
Latin American 2 Sub 610 C=1.000 G=0.000
South Asian Sub 94 C=1.00 G=0.00
Other Sub 466 C=1.000 G=0.000


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 C=0.999996 G=0.000004
gnomAD - Genomes Global Study-wide 140280 C=0.999993 G=0.000007
gnomAD - Genomes European Sub 75948 C=0.99999 G=0.00001
gnomAD - Genomes African Sub 42058 C=1.00000 G=0.00000
gnomAD - Genomes American Sub 13664 C=1.00000 G=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3324 C=1.0000 G=0.0000
gnomAD - Genomes East Asian Sub 3132 C=1.0000 G=0.0000
gnomAD - Genomes Other Sub 2154 C=1.0000 G=0.0000
ExAC Global Study-wide 121392 C=0.999992 T=0.000008
ExAC Europe Sub 73336 C=1.00000 T=0.00000
ExAC Asian Sub 25166 C=0.99996 T=0.00004
ExAC American Sub 11578 C=1.00000 T=0.00000
ExAC African Sub 10404 C=1.00000 T=0.00000
ExAC Other Sub 908 C=1.000 T=0.000
Allele Frequency Aggregator Total Global 10680 C=1.00000 G=0.00000
Allele Frequency Aggregator European Sub 6962 C=1.0000 G=0.0000
Allele Frequency Aggregator African Sub 2294 C=1.0000 G=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 C=1.000 G=0.000
Allele Frequency Aggregator Other Sub 466 C=1.000 G=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 C=1.000 G=0.000
Allele Frequency Aggregator Asian Sub 108 C=1.000 G=0.000
Allele Frequency Aggregator South Asian Sub 94 C=1.00 G=0.00
KOREAN population from KRGDB KOREAN Study-wide 2922 C=0.9997 T=0.0003
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 11 NC_000011.10:g.47235304C>G
GRCh38.p14 chr 11 NC_000011.10:g.47235304C>T
GRCh37.p13 chr 11 NC_000011.9:g.47256855C>G
GRCh37.p13 chr 11 NC_000011.9:g.47256855C>T
DDB2 RefSeqGene (LRG_467) NG_009365.1:g.25363C>G
DDB2 RefSeqGene (LRG_467) NG_009365.1:g.25363C>T
Gene: DDB2, damage specific DNA binding protein 2 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
DDB2 transcript variant D1 NM_001300734.2:c.457-2533…

NM_001300734.2:c.457-2533C>G

N/A Intron Variant
DDB2 transcript variant 5 NM_001399876.1:c.457-2533…

NM_001399876.1:c.457-2533C>G

N/A Intron Variant
DDB2 transcript variant WT NM_000107.3:c.915C>G T [ACC] > T [ACG] Coding Sequence Variant
DNA damage-binding protein 2 isoform WT NP_000098.1:p.Thr305= T (Thr) > T (Thr) Synonymous Variant
DDB2 transcript variant WT NM_000107.3:c.915C>T T [ACC] > T [ACT] Coding Sequence Variant
DNA damage-binding protein 2 isoform WT NP_000098.1:p.Thr305= T (Thr) > T (Thr) Synonymous Variant
DDB2 transcript variant 6 NM_001399878.1:c.723C>G T [ACC] > T [ACG] Coding Sequence Variant
DNA damage-binding protein 2 isoform 3 NP_001386807.1:p.Thr241= T (Thr) > T (Thr) Synonymous Variant
DDB2 transcript variant 6 NM_001399878.1:c.723C>T T [ACC] > T [ACT] Coding Sequence Variant
DNA damage-binding protein 2 isoform 3 NP_001386807.1:p.Thr241= T (Thr) > T (Thr) Synonymous Variant
DDB2 transcript variant 4 NM_001399875.1:c.915C>G T [ACC] > T [ACG] Coding Sequence Variant
DNA damage-binding protein 2 isoform WT NP_001386804.1:p.Thr305= T (Thr) > T (Thr) Synonymous Variant
DDB2 transcript variant 4 NM_001399875.1:c.915C>T T [ACC] > T [ACT] Coding Sequence Variant
DNA damage-binding protein 2 isoform WT NP_001386804.1:p.Thr305= T (Thr) > T (Thr) Synonymous Variant
DDB2 transcript variant 3 NM_001399874.1:c.915C>G T [ACC] > T [ACG] Coding Sequence Variant
DNA damage-binding protein 2 isoform WT NP_001386803.1:p.Thr305= T (Thr) > T (Thr) Synonymous Variant
DDB2 transcript variant 3 NM_001399874.1:c.915C>T T [ACC] > T [ACT] Coding Sequence Variant
DNA damage-binding protein 2 isoform WT NP_001386803.1:p.Thr305= T (Thr) > T (Thr) Synonymous Variant
DDB2 transcript variant 7 NR_174610.1:n.1166C>G N/A Non Coding Transcript Variant
DDB2 transcript variant 7 NR_174610.1:n.1166C>T N/A Non Coding Transcript Variant
DDB2 transcript variant 8 NR_174611.1:n.1144C>G N/A Non Coding Transcript Variant
DDB2 transcript variant 8 NR_174611.1:n.1144C>T N/A Non Coding Transcript Variant
DDB2 transcript variant X1 XM_047426487.1:c.*2= N/A 3 Prime UTR 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.

Allele: G (allele ID: 1684595 )
ClinVar Accession Disease Names Clinical Significance
RCV002259196.1 Xeroderma pigmentosum Likely-Benign
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 11 NC_000011.10:g.47235304= NC_000011.10:g.47235304C>G NC_000011.10:g.47235304C>T
GRCh37.p13 chr 11 NC_000011.9:g.47256855= NC_000011.9:g.47256855C>G NC_000011.9:g.47256855C>T
DDB2 RefSeqGene (LRG_467) NG_009365.1:g.25363= NG_009365.1:g.25363C>G NG_009365.1:g.25363C>T
DDB2 transcript variant WT NM_000107.3:c.915= NM_000107.3:c.915C>G NM_000107.3:c.915C>T
DDB2 transcript variant WT NM_000107.2:c.915= NM_000107.2:c.915C>G NM_000107.2:c.915C>T
DDB2 transcript variant 3 NM_001399874.1:c.915= NM_001399874.1:c.915C>G NM_001399874.1:c.915C>T
DDB2 transcript variant 4 NM_001399875.1:c.915= NM_001399875.1:c.915C>G NM_001399875.1:c.915C>T
DDB2 transcript variant 7 NR_174610.1:n.1166= NR_174610.1:n.1166C>G NR_174610.1:n.1166C>T
DDB2 transcript variant 8 NR_174611.1:n.1144= NR_174611.1:n.1144C>G NR_174611.1:n.1144C>T
DDB2 transcript variant 6 NM_001399878.1:c.723= NM_001399878.1:c.723C>G NM_001399878.1:c.723C>T
DDB2 transcript variant X1 XM_047426487.1:c.*2= XM_047426487.1:c.*2C>G XM_047426487.1:c.*2C>T
DNA damage-binding protein 2 isoform WT NP_000098.1:p.Thr305= NP_000098.1:p.Thr305= NP_000098.1:p.Thr305=
DNA damage-binding protein 2 isoform WT NP_001386803.1:p.Thr305= NP_001386803.1:p.Thr305= NP_001386803.1:p.Thr305=
DNA damage-binding protein 2 isoform WT NP_001386804.1:p.Thr305= NP_001386804.1:p.Thr305= NP_001386804.1:p.Thr305=
DNA damage-binding protein 2 isoform 3 NP_001386807.1:p.Thr241= NP_001386807.1:p.Thr241= NP_001386807.1:p.Thr241=
DDB2 transcript variant D1 NM_001300734.2:c.457-2533= NM_001300734.2:c.457-2533C>G NM_001300734.2:c.457-2533C>T
DDB2 transcript variant 5 NM_001399876.1:c.457-2533= NM_001399876.1:c.457-2533C>G NM_001399876.1:c.457-2533C>T
DDB2 transcript variant X2 XM_005252808.1:c.457-2533= XM_005252808.1:c.457-2533C>G XM_005252808.1:c.457-2533C>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#.

5 SubSNP, 7 Frequency, 1 ClinVar submissions
No Submitter Submission ID Date (Build)
1 EVA_EXAC ss1690345668 Apr 01, 2015 (144)
2 GNOMAD ss2738935569 Nov 08, 2017 (151)
3 KRGDB ss3924468924 Apr 26, 2020 (154)
4 GNOMAD ss4234583561 Apr 26, 2021 (155)
5 TOPMED ss4884334654 Apr 26, 2021 (155)
6 ExAC NC_000011.9 - 47256855 Oct 12, 2018 (152)
7 gnomAD - Genomes NC_000011.10 - 47235304 Apr 26, 2021 (155)
8 gnomAD - Exomes

Submission ignored due to conflicting rows:
Row 8148509 (NC_000011.9:47256854:C:C 251475/251476, NC_000011.9:47256854:C:G 1/251476)
Row 8148510 (NC_000011.9:47256854:C:C 251475/251476, NC_000011.9:47256854:C:T 1/251476)

- Jul 13, 2019 (153)
9 gnomAD - Exomes

Submission ignored due to conflicting rows:
Row 8148509 (NC_000011.9:47256854:C:C 251475/251476, NC_000011.9:47256854:C:G 1/251476)
Row 8148510 (NC_000011.9:47256854:C:C 251475/251476, NC_000011.9:47256854:C:T 1/251476)

- Jul 13, 2019 (153)
10 KOREAN population from KRGDB NC_000011.9 - 47256855 Apr 26, 2020 (154)
11 TopMed NC_000011.10 - 47235304 Apr 26, 2021 (155)
12 ALFA NC_000011.10 - 47235304 Apr 26, 2021 (155)
13 ClinVar RCV002259196.1 Oct 16, 2022 (156)
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
ss2738935569 NC_000011.9:47256854:C:G NC_000011.10:47235303:C:G (self)
RCV002259196.1, 378891299, 99880310, 10525039699, ss4234583561, ss4884334654 NC_000011.10:47235303:C:G NC_000011.10:47235303:C:G (self)
600215, 31646318, ss1690345668, ss2738935569, ss3924468924 NC_000011.9:47256854:C:T NC_000011.10:47235303: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 rs758199547

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.post761+d5e8e07