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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.

rs769656679

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:13538 (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
G>A / G>T
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.000172 (21/121866, GnomAD)
A=0.00007 (6/91862, GnomAD_exome)
A=0.00022 (4/17954, ALFA) (+ 4 more)
A=0.02315 (388/16760, 8.3KJPN)
A=0.0092 (27/2922, KOREAN)
A=0.0004 (1/2784, ExAC)
A=0.0000 (0/1828, Korea1K)
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.13538G>A
GRCh38.p13 chr 1 NC_000001.11:g.13538G>T
GRCh37.p13 chr 1 NC_000001.10:g.13538G>A
GRCh37.p13 chr 1 NC_000001.10:g.13538G>T
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.781G>A N/A Non Coding Transcript Variant
DDX11L1 transcript NR_046018.2:n.781G>T 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 (New)
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 17954 G=0.99978 A=0.00022
European Sub 13190 G=0.99985 A=0.00015
African Sub 2888 G=1.0000 A=0.0000
African Others Sub 110 G=1.000 A=0.000
African American Sub 2778 G=1.0000 A=0.0000
Asian Sub 132 G=1.000 A=0.000
East Asian Sub 96 G=1.00 A=0.00
Other Asian Sub 36 G=1.00 A=0.00
Latin American 1 Sub 146 G=0.993 A=0.007
Latin American 2 Sub 610 G=0.998 A=0.002
South Asian Sub 94 G=1.00 A=0.00
Other Sub 894 G=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").

Download
Study Population Group Sample Size Ref Allele Alt Allele
gnomAD - Genomes Global Study-wide 121866 G=0.999828 A=0.000172
gnomAD - Genomes European Sub 62350 G=0.99978 A=0.00022
gnomAD - Genomes African Sub 40828 G=0.99993 A=0.00007
gnomAD - Genomes American Sub 11224 G=0.99964 A=0.00036
gnomAD - Genomes East Asian Sub 3014 G=1.0000 A=0.0000
gnomAD - Genomes Ashkenazi Jewish Sub 2654 G=1.0000 A=0.0000
gnomAD - Genomes Other Sub 1796 G=1.0000 A=0.0000
gnomAD - Exomes Global Study-wide 91862 G=0.99993 A=0.00007
gnomAD - Exomes European Sub 37060 G=0.99992 A=0.00008
gnomAD - Exomes Asian Sub 23786 G=1.00000 A=0.00000
gnomAD - Exomes American Sub 17628 G=1.00000 A=0.00000
gnomAD - Exomes African Sub 6130 G=1.0000 A=0.0000
gnomAD - Exomes Ashkenazi Jewish Sub 4286 G=1.0000 A=0.0000
gnomAD - Exomes Other Sub 2972 G=0.9990 A=0.0010
8.3KJPN JAPANESE Study-wide 16760 G=0.97685 A=0.02315
KOREAN population from KRGDB KOREAN Study-wide 2922 G=0.9908 A=0.0092
ExAC Global Study-wide 2784 G=0.9996 A=0.0004
ExAC Asian Sub 1686 G=1.0000 A=0.0000
ExAC Europe Sub 746 G=1.000 A=0.000
ExAC African Sub 266 G=1.000 A=0.000
ExAC American Sub 48 G=1.00 A=0.00
ExAC Other Sub 38 G=0.97 A=0.03
Korean Genome Project KOREAN Study-wide 1828 G=1.0000 A=0.0000
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 G= A T
GRCh38.p13 chr 1 NC_000001.11:g.13538= NC_000001.11:g.13538G>A NC_000001.11:g.13538G>T
GRCh37.p13 chr 1 NC_000001.10:g.13538= NC_000001.10:g.13538G>A NC_000001.10:g.13538G>T
DDX11L1 transcript NR_046018.2:n.781= NR_046018.2:n.781G>A NR_046018.2:n.781G>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#.

9 SubSNP, 7 Frequency submissions
No Submitter Submission ID Date (Build)
1 EVA_EXAC ss1685216844 Apr 01, 2015 (144)
2 GNOMAD ss2730985367 Nov 08, 2017 (151)
3 GNOMAD ss2746168645 Nov 08, 2017 (151)
4 GNOMAD ss2750601185 Nov 08, 2017 (151)
5 SWEGEN ss2986141265 Nov 08, 2017 (151)
6 TOPMED ss3066316515 Nov 08, 2017 (151)
7 KRGDB ss3892822827 Apr 25, 2020 (154)
8 KOGIC ss3943622079 Apr 25, 2020 (154)
9 TOMMO_GENOMICS ss5142031070 Apr 25, 2021 (155)
10 ExAC NC_000001.10 - 13538 Oct 11, 2018 (152)
11 gnomAD - Genomes NC_000001.11 - 13538 Apr 25, 2021 (155)
12 gnomAD - Exomes NC_000001.10 - 13538 Jul 12, 2019 (153)
13 KOREAN population from KRGDB NC_000001.10 - 13538 Apr 25, 2020 (154)
14 Korean Genome Project NC_000001.11 - 13538 Apr 25, 2020 (154)
15 8.3KJPN NC_000001.10 - 13538 Apr 25, 2021 (155)
16 ALFA NC_000001.11 - 13538 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
4389914, 39, 221, 377, ss1685216844, ss2730985367, ss2746168645, ss2750601185, ss2986141265, ss3892822827, ss5142031070 NC_000001.10:13537:G:A NC_000001.11:13537:G:A (self)
819, 80, 13835931589, ss3066316515, ss3943622079 NC_000001.11:13537:G:A NC_000001.11:13537:G:A (self)
ss2730985367 NC_000001.10:13537:G:T NC_000001.11:13537:G: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 rs769656679

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