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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.


Current Build 155

Released April 9, 2021

Homo sapiens
chr1:13543 (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.

Variation Type
SNV Single Nucleotide Variation
G=0.000057 (7/122900, GnomAD)
G=0.00015 (13/84650, GnomAD_exome)
G=0.00030 (5/16760, 8.3KJPN) (+ 5 more)
G=0.00000 (0/11862, ALFA)
G=0.0006 (3/5008, 1000G)
G=0.0010 (3/2922, KOREAN)
G=0.0016 (3/1828, Korea1K)
G=0.001 (1/990, ExAC)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
DDX11L1 : Non Coding Transcript Variant
0 citations
Genomic View
See rs on genome

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.13543T>G
GRCh37.p13 chr 1 NC_000001.10:g.13543T>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.786T>G N/A Non Coding 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.

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 11862 T=1.00000 G=0.00000
European Sub 7618 T=1.0000 G=0.0000
African Sub 2816 T=1.0000 G=0.0000
African Others Sub 108 T=1.000 G=0.000
African American Sub 2708 T=1.0000 G=0.0000
Asian Sub 108 T=1.000 G=0.000
East Asian Sub 84 T=1.00 G=0.00
Other Asian Sub 24 T=1.00 G=0.00
Latin American 1 Sub 146 T=1.000 G=0.000
Latin American 2 Sub 610 T=1.000 G=0.000
South Asian Sub 94 T=1.00 G=0.00
Other Sub 470 T=1.000 G=0.000


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").

Study Population Group Sample Size Ref Allele Alt Allele
gnomAD - Genomes Global Study-wide 122900 T=0.999943 G=0.000057
gnomAD - Genomes European Sub 63104 T=1.00000 G=0.00000
gnomAD - Genomes African Sub 40946 T=1.00000 G=0.00000
gnomAD - Genomes American Sub 11338 T=1.00000 G=0.00000
gnomAD - Genomes East Asian Sub 3024 T=0.9977 G=0.0023
gnomAD - Genomes Ashkenazi Jewish Sub 2670 T=1.0000 G=0.0000
gnomAD - Genomes Other Sub 1818 T=1.0000 G=0.0000
gnomAD - Exomes Global Study-wide 84650 T=0.99985 G=0.00015
gnomAD - Exomes European Sub 33496 T=1.00000 G=0.00000
gnomAD - Exomes Asian Sub 21926 T=0.99941 G=0.00059
gnomAD - Exomes American Sub 16912 T=1.00000 G=0.00000
gnomAD - Exomes African Sub 6030 T=1.0000 G=0.0000
gnomAD - Exomes Ashkenazi Jewish Sub 3536 T=1.0000 G=0.0000
gnomAD - Exomes Other Sub 2750 T=1.0000 G=0.0000
8.3KJPN JAPANESE Study-wide 16760 T=0.99970 G=0.00030
1000Genomes Global Study-wide 5008 T=0.9994 G=0.0006
1000Genomes African Sub 1322 T=1.0000 G=0.0000
1000Genomes East Asian Sub 1008 T=0.9970 G=0.0030
1000Genomes Europe Sub 1006 T=1.0000 G=0.0000
1000Genomes South Asian Sub 978 T=1.000 G=0.000
1000Genomes American Sub 694 T=1.000 G=0.000
KOREAN population from KRGDB KOREAN Study-wide 2922 T=0.9990 G=0.0010
Korean Genome Project KOREAN Study-wide 1828 T=0.9984 G=0.0016
ExAC Global Study-wide 990 T=0.999 G=0.001
ExAC Asian Sub 468 T=0.998 G=0.002
ExAC Europe Sub 266 T=1.000 G=0.000
ExAC African Sub 208 T=1.000 G=0.000
ExAC American Sub 32 T=1.00 G=0.00
ExAC Other Sub 16 T=1.00 G=0.00

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 T= G
GRCh38.p13 chr 1 NC_000001.11:g.13543= NC_000001.11:g.13543T>G
GRCh37.p13 chr 1 NC_000001.10:g.13543= NC_000001.10:g.13543T>G
DDX11L1 transcript NR_046018.2:n.786= NR_046018.2:n.786T>G

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#.

10 SubSNP, 8 Frequency submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss1289335468 Aug 21, 2014 (142)
2 EVA_EXAC ss1685216846 Apr 01, 2015 (144)
3 GNOMAD ss2730985371 Nov 08, 2017 (151)
4 GNOMAD ss2746168647 Nov 08, 2017 (151)
5 GNOMAD ss2750601187 Nov 08, 2017 (151)
6 TOPMED ss3066316518 Nov 08, 2017 (151)
7 KHV_HUMAN_GENOMES ss3798742401 Jul 12, 2019 (153)
8 KRGDB ss3892822828 Apr 25, 2020 (154)
9 KOGIC ss3943622080 Apr 25, 2020 (154)
10 TOMMO_GENOMICS ss5142031071 Apr 25, 2021 (155)
11 1000Genomes NC_000001.10 - 13543 Oct 11, 2018 (152)
12 ExAC NC_000001.10 - 13543 Oct 11, 2018 (152)
13 gnomAD - Genomes NC_000001.11 - 13543 Apr 25, 2021 (155)
14 gnomAD - Exomes NC_000001.10 - 13543 Jul 12, 2019 (153)
15 KOREAN population from KRGDB NC_000001.10 - 13543 Apr 25, 2020 (154)
16 Korean Genome Project NC_000001.11 - 13543 Apr 25, 2020 (154)
17 8.3KJPN NC_000001.10 - 13543 Apr 25, 2021 (155)
18 ALFA NC_000001.11 - 13543 Apr 25, 2021 (155)

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
34, 4389916, 40, 222, 378, ss1289335468, ss1685216846, ss2730985371, ss2746168647, ss2750601187, ss3892822828, ss5142031071 NC_000001.10:13542:T:G NC_000001.11:13542:T:G (self)
821, 81, 6331970618, ss3066316518, ss3798742401, ss3943622080 NC_000001.11:13542:T:G NC_000001.11:13542:T:G (self)

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

No publications for rs540466151


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