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dbSNP Short Genetic Variations

Reference SNP (rs) Report

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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.

rs780379327

Current Build 152

Released October 2, 2018

Organism
Homo sapiens
Position
chr1:13486-13487 (GRCh38.p12) 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
delGC
Variation Type
Deletion
Frequency
delGC=0.0000 (1/29800, GnomAD)
delGC=0.0000 (0/11790, ExAC)
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.p12 chr 1 NC_000001.11:g.13486_13487delGC
GRCh37.p13 chr 1 NC_000001.10:g.13486_13487delGC
Gene: DDX11L1, DEAD/H-box helicase 11 like 1 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
DDX11L1 transcript NR_046018.2:n.729_730delGC 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
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
gnomAD - Genomes Global Study-wide 29800 GC=1.0000 delGC=0.0000
gnomAD - Genomes European Sub 17488 GC=0.9999 delGC=0.0001
gnomAD - Genomes African Sub 8732 GC=1.000 delGC=0.000
gnomAD - Genomes East Asian Sub 1618 GC=1.000 delGC=0.000
gnomAD - Genomes Other Sub 926 GC=1.00 delGC=0.00
gnomAD - Genomes American Sub 796 GC=1.00 delGC=0.00
gnomAD - Genomes Ashkenazi Jewish Sub 240 GC=1.00 delGC=0.00
ExAC Global Study-wide 11790 GC=1.0000 delGC=0.0000
ExAC Asian Sub 7746 GC=1.000 delGC=0.000
ExAC Europe Sub 3124 GC=1.000 delGC=0.000
ExAC African Sub 644 GC=1.00 delGC=0.00
ExAC American Sub 152 GC=1.00 delGC=0.00
ExAC Other Sub 124 GC=1.00 delGC=0.00
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 GC= delGC Note
GRCh38.p12 chr 1 NC_000001.11:g.13486_13...

NC_000001.11:g.13486_13487GC=

NC_000001.11:g.13486_13...

NC_000001.11:g.13486_13487delGC

GRCh37.p13 chr 1 NC_000001.10:g.13486_13...

NC_000001.10:g.13486_13487GC=

NC_000001.10:g.13486_13...

NC_000001.10:g.13486_13487delGC

DDX11L1 transcript NR_046018.2:n.729_730GC= NR_046018.2:n.729_730delGC
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#.

2 Frequency, 5 SubSNP submissions
No Submitter Submission ID Date (Build)
1 EVA_EXAC ss1711595247 Apr 01, 2015 (144)
2 GNOMAD ss2730985342 Nov 08, 2017 (151)
3 GNOMAD ss2746168626 Nov 08, 2017 (151)
4 GNOMAD ss2750601166 Nov 08, 2017 (151)
5 TOPMED ss3066316496 Nov 08, 2017 (151)
6 ExAC NC_000001.10 - 13486 Oct 11, 2018 (152)
7 gnomAD - Genomes NC_000001.10 - 13486 Oct 11, 2018 (152)
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
4389904, 365, ss1711595247, ss2730985342, ss2746168626, ss2750601166 NC_000001.10:13485:GC= NC_000001.11:13485:GC= (self)
ss3066316496 NC_000001.11:13485:GC= NC_000001.11:13485:GC= (self)
4389904, 365, ss1711595247, ss2730985342, ss2746168626, ss2750601166 NC_000001.10:13485:delGC NC_000001.11:13485:delGC (self)
ss3066316496 NC_000001.11:13485:delGC NC_000001.11:13485:delGC (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 rs780379327

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.post12+6d211b7