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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.

rs538606945

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:13382 (GRCh38.p13) 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>A / C>G
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.000004 (1/264690, TOPMED)
A=0.000009 (1/113690, GnomAD)
G=0.00001 (1/94440, GnomAD_exome) (+ 3 more)
A=0.00000 (0/10680, ALFA)
G=0.0002 (1/5728, ExAC)
G=0.0002 (1/5008, 1000G)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
DDX11L1 : Non Coding Transcript Variant
Publications
0 citations
Genomic View
See rs on genome
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.p13 chr 1 NC_000001.11:g.13382C>A
GRCh38.p13 chr 1 NC_000001.11:g.13382C>G
GRCh37.p13 chr 1 NC_000001.10:g.13382C>A
GRCh37.p13 chr 1 NC_000001.10:g.13382C>G
Gene: DDX11L1, DEAD/H-box helicase 11 like 1 (pseudogene) (plus strand)
Molecule type Change Amino acid[Codon] SO Term
DDX11L1 transcript NR_046018.2:n.625C>A N/A Non Coding Transcript Variant
DDX11L1 transcript NR_046018.2:n.625C>G 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

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: 20201027095038
Population Group Sample Size Ref Allele Alt Allele
Total Global 10680 C=1.00000 A=0.00000
European Sub 6962 C=1.0000 A=0.0000
African Sub 2294 C=1.0000 A=0.0000
African Others Sub 84 C=1.00 A=0.00
African American Sub 2210 C=1.0000 A=0.0000
Asian Sub 108 C=1.000 A=0.000
East Asian Sub 84 C=1.00 A=0.00
Other Asian Sub 24 C=1.00 A=0.00
Latin American 1 Sub 146 C=1.000 A=0.000
Latin American 2 Sub 610 C=1.000 A=0.000
South Asian Sub 94 C=1.00 A=0.00
Other Sub 466 C=1.000 A=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").

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Study Population Group Sample Size Ref Allele Alt Allele
TopMed Global Study-wide 264690 C=0.999996 A=0.000004
gnomAD - Genomes Global Study-wide 113690 C=0.999991 A=0.000009
gnomAD - Genomes European Sub 57940 C=1.00000 A=0.00000
gnomAD - Genomes African Sub 38490 C=0.99997 A=0.00003
gnomAD - Genomes American Sub 10158 C=1.00000 A=0.00000
gnomAD - Genomes East Asian Sub 2946 C=1.0000 A=0.0000
gnomAD - Genomes Ashkenazi Jewish Sub 2458 C=1.0000 A=0.0000
gnomAD - Genomes Other Sub 1698 C=1.0000 A=0.0000
gnomAD - Exomes Global Study-wide 94440 C=0.99999 G=0.00001
gnomAD - Exomes European Sub 39038 C=1.00000 G=0.00000
gnomAD - Exomes Asian Sub 25364 C=0.99996 G=0.00004
gnomAD - Exomes American Sub 16014 C=1.00000 G=0.00000
gnomAD - Exomes African Sub 6266 C=1.0000 G=0.0000
gnomAD - Exomes Ashkenazi Jewish Sub 4674 C=1.0000 G=0.0000
gnomAD - Exomes Other Sub 3084 C=1.0000 G=0.0000
ExAC Global Study-wide 5728 C=0.9998 G=0.0002
ExAC Asian Sub 3722 C=0.9997 G=0.0003
ExAC Europe Sub 1404 C=1.0000 G=0.0000
ExAC African Sub 460 C=1.000 G=0.000
ExAC American Sub 82 C=1.00 G=0.00
ExAC Other Sub 60 C=1.00 G=0.00
1000Genomes Global Study-wide 5008 C=0.9998 G=0.0002
1000Genomes African Sub 1322 C=1.0000 G=0.0000
1000Genomes East Asian Sub 1008 C=1.0000 G=0.0000
1000Genomes Europe Sub 1006 C=1.0000 G=0.0000
1000Genomes South Asian Sub 978 C=0.999 G=0.001
1000Genomes American Sub 694 C=1.000 G=0.000
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= A G
GRCh38.p13 chr 1 NC_000001.11:g.13382= NC_000001.11:g.13382C>A NC_000001.11:g.13382C>G
GRCh37.p13 chr 1 NC_000001.10:g.13382= NC_000001.10:g.13382C>A NC_000001.10:g.13382C>G
DDX11L1 transcript NR_046018.2:n.625= NR_046018.2:n.625C>A NR_046018.2:n.625C>G
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, 6 Frequency submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss1289335462 Aug 21, 2014 (142)
2 EVA_EXAC ss1685216822 Apr 01, 2015 (144)
3 GNOMAD ss2730985304 Nov 08, 2017 (151)
4 GNOMAD ss3986889518 Apr 25, 2021 (155)
5 TOPMED ss4436393783 Apr 25, 2021 (155)
6 1000Genomes NC_000001.10 - 13382 Oct 11, 2018 (152)
7 ExAC NC_000001.10 - 13382 Oct 11, 2018 (152)
8 gnomAD - Genomes NC_000001.11 - 13382 Apr 25, 2021 (155)
9 gnomAD - Exomes NC_000001.10 - 13382 Jul 12, 2019 (153)
10 TopMed NC_000001.11 - 13382 Apr 25, 2021 (155)
11 ALFA NC_000001.11 - 13382 Apr 25, 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
782, 118, 9455239442, ss3986889518, ss4436393783 NC_000001.11:13381:C:A NC_000001.11:13381:C:A
28, 4389890, 15, ss1289335462, ss1685216822, ss2730985304 NC_000001.10:13381:C:G NC_000001.11:13381:C:G (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 rs538606945

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.post596+ae089ad