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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.

rs779258992

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:10147-10150 (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
delCC / delC
Variation Type
Indel Insertion and Deletion
Frequency
delC=0.11111 (1318/11862, ALFA)
delC=0.1544 (1476/9558, 8.3KJPN)
delC=0.0719 (118/1642, Korea1K)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
DDX11L1 : 2KB Upstream 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.10149_10150del
GRCh38.p13 chr 1 NC_000001.11:g.10150del
GRCh37.p13 chr 1 NC_000001.10:g.10149_10150del
GRCh37.p13 chr 1 NC_000001.10:g.10150del
Gene: DDX11L1, DEAD/H-box helicase 11 like 1 (pseudogene) (plus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
DDX11L1 transcript NR_046018.2: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

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 CCCC=0.88889 CCC=0.11111
European Sub 7618 CCCC=0.8773 CCC=0.1227
African Sub 2816 CCCC=0.9247 CCC=0.0753
African Others Sub 108 CCCC=0.907 CCC=0.093
African American Sub 2708 CCCC=0.9254 CCC=0.0746
Asian Sub 108 CCCC=0.843 CCC=0.157
East Asian Sub 84 CCCC=0.87 CCC=0.13
Other Asian Sub 24 CCCC=0.75 CCC=0.25
Latin American 1 Sub 146 CCCC=0.856 CCC=0.144
Latin American 2 Sub 610 CCCC=0.884 CCC=0.116
South Asian Sub 94 CCCC=0.86 CCC=0.14
Other Sub 470 CCCC=0.896 CCC=0.104


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
8.3KJPN JAPANESE Study-wide 9558 (C)4=0.8456 delC=0.1544
Korean Genome Project KOREAN Study-wide 1642 (C)4=0.9281 delC=0.0719
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)4= delCC delC
GRCh38.p13 chr 1 NC_000001.11:g.10147_10150= NC_000001.11:g.10149_10150del NC_000001.11:g.10150del
GRCh37.p13 chr 1 NC_000001.10:g.10147_10150= NC_000001.10:g.10149_10150del NC_000001.10:g.10150del
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#.

7 SubSNP, 5 Frequency submissions
No Submitter Submission ID Date (Build)
1 SSMP ss663103904 Apr 01, 2015 (144)
2 SWEGEN ss2137518744 Nov 08, 2017 (151)
3 TOPMED ss3066315846 Nov 08, 2017 (151)
4 KOGIC ss3943622004 Apr 25, 2020 (154)
5 GNOMAD ss3986889035 Apr 25, 2021 (155)
6 GNOMAD ss3986889036 Apr 25, 2021 (155)
7 TOMMO_GENOMICS ss5142030703 Apr 25, 2021 (155)
8 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 39 (NC_000001.11:10146:C: 9686/15324)
Row 40 (NC_000001.11:10146:CC: 2/15326)

- Apr 25, 2021 (155)
9 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 39 (NC_000001.11:10146:C: 9686/15324)
Row 40 (NC_000001.11:10146:CC: 2/15326)

- Apr 25, 2021 (155)
10 Korean Genome Project NC_000001.11 - 10148 Apr 25, 2020 (154)
11 8.3KJPN NC_000001.10 - 10147 Apr 25, 2021 (155)
12 ALFA NC_000001.11 - 10147 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
ss3986889036 NC_000001.11:10146:CC: NC_000001.11:10146:CCCC:CC
10, ss663103904, ss2137518744, ss5142030703 NC_000001.10:10146:C: NC_000001.11:10146:CCCC:CCC (self)
ss3066315846, ss3986889035 NC_000001.11:10146:C: NC_000001.11:10146:CCCC:CCC (self)
3256707139 NC_000001.11:10146:CCCC:CCC NC_000001.11:10146:CCCC:CCC
5, ss3943622004 NC_000001.11:10147:C: NC_000001.11:10146:CCCC:CCC (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 rs779258992

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