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dbSNP Short Genetic Variations

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.

rs387906866

Current Build 153

Released July 9, 2019

Organism
Homo sapiens
Position
chr2:9527799-9527805 (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
delGTCT
Variation Type
Indel Insertion and Deletion
Frequency
None
Clinical Significance
Reported in ClinVar
Gene : Consequence
ADAM17 : Frameshift
Publications
1 citation
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 2 NC_000002.12:g.9527802_9527805del
GRCh37.p13 chr 2 NC_000002.11:g.9667931_9667934del
ADAM17 RefSeqGene (LRG_1203) NG_029873.1:g.32987_32990del
Gene: ADAM17, ADAM metallopeptidase domain 17 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
ADAM17 transcript NM_003183.6:c.603_606del D [GAC] > E [GA] Coding Sequence Variant
disintegrin and metalloproteinase domain-containing protein 17 preproprotein NP_003174.3:p.Asp201fs D (Asp) > E (Glu) Frameshift
ADAM17 transcript variant X2 XM_011510376.3:c. N/A 5 Prime UTR Variant
ADAM17 transcript variant X3 XM_017004785.2:c. N/A 5 Prime UTR Variant
ADAM17 transcript variant X4 XM_024453056.1:c. N/A 5 Prime UTR Variant
ADAM17 transcript variant X5 XM_017004786.2:c. N/A 5 Prime UTR Variant
ADAM17 transcript variant X1 XM_011510375.3:c.510_51...

XM_011510375.3:c.510_513del

D [GAC] > E [GA] Coding Sequence Variant
disintegrin and metalloproteinase domain-containing protein 17 isoform X1 XP_011508677.1:p.Asp170fs D (Asp) > E (Glu) Frameshift
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.

Allele: delGTCT (allele ID: 39331 )
ClinVar Accession Disease Names Clinical Significance
RCV000023322.5 Inflammatory skin and bowel disease, neonatal 1 Pathogenic
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").

None
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 TCTGTCT= delGTCT Note
GRCh38.p12 chr 2 NC_000002.12:g.9527799_...

NC_000002.12:g.9527799_9527805=

NC_000002.12:g.9527802_...

NC_000002.12:g.9527802_9527805del

GRCh37.p13 chr 2 NC_000002.11:g.9667928_...

NC_000002.11:g.9667928_9667934=

NC_000002.11:g.9667931_...

NC_000002.11:g.9667931_9667934del

ADAM17 RefSeqGene (LRG_1203) NG_029873.1:g.32984_32990= NG_029873.1:g.32987_329...

NG_029873.1:g.32987_32990del

ADAM17 transcript NM_003183.6:c.600_606= NM_003183.6:c.603_606del
ADAM17 transcript NM_003183.5:c.600_606= NM_003183.5:c.603_606del
ADAM17 transcript NM_003183.4:c.600_606= NM_003183.4:c.603_606del
ADAM17 transcript variant X1 XM_011510375.3:c.507_513= XM_011510375.3:c.510_51...

XM_011510375.3:c.510_513del

ADAM17 transcript variant X2 XM_011510376.3:c.-81_-75= XM_011510376.3:c.-78_-7...

XM_011510376.3:c.-78_-75del

ADAM17 transcript variant X3 XM_017004785.2:c.-303_-...

XM_017004785.2:c.-303_-297=

XM_017004785.2:c.-300_-...

XM_017004785.2:c.-300_-297del

ADAM17 transcript variant X5 XM_017004786.2:c.-323_-...

XM_017004786.2:c.-323_-317=

XM_017004786.2:c.-320_-...

XM_017004786.2:c.-320_-317del

ADAM17 transcript variant X4 XM_024453056.1:c.-2250_...

XM_024453056.1:c.-2250_-2244=

XM_024453056.1:c.-2247_...

XM_024453056.1:c.-2247_-2244del

disintegrin and metalloproteinase domain-containing protein 17 preproprotein NP_003174.3:p.Val200_Ar...

NP_003174.3:p.Val200_Arg202=

NP_003174.3:p.Asp201fs
disintegrin and metalloproteinase domain-containing protein 17 isoform X1 XP_011508677.1:p.Val169...

XP_011508677.1:p.Val169_Arg171=

XP_011508677.1:p.Asp170fs
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#.

1 SubSNP, 1 ClinVar submissions
No Submitter Submission ID Date (Build)
1 OMIM-CURATED-RECORDS ss825077461 Jun 20, 2013 (137)
2 ClinVar RCV000023322.5 Jul 12, 2019 (153)
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
RCV000023322.5, ss825077461 NC_000002.12:9527798:TCTG: NC_000002.12:9527798:TCTGTCT:TCT (self)
Help

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

1 citation for rs387906866
PMID Title Author Year Journal
22010916 Inflammatory skin and bowel disease linked to ADAM17 deletion. Blaydon DC et al. 2011 The New England journal of medicine

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.post246+3cda961