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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.

rs63749858

Current Build 153

Released July 9, 2019

Organism
Homo sapiens
Position
chr11:5225611 (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
delT
Variation Type
Deletion
Frequency
None
Clinical Significance
Reported in ClinVar
Gene : Consequence
HBB : Frameshift
Publications
2 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 11 NC_000011.10:g.5225611del
GRCh37.p13 chr 11 NC_000011.9:g.5246841del
HBB region RefSeqGene NG_000007.3:g.72005del
HBB RefSeqGene NG_059281.1:g.6461del
LOC107133510 genomic region NG_046672.1:g.3546del
LOC110006319 genomic region NG_053049.1:g.1932del
Gene: HBB, hemoglobin subunit beta (minus strand)
Molecule type Change Amino acid[Codon] SO Term
HBB transcript NM_000518.5:c.431del H [CAC] > P [CC] Coding Sequence Variant
hemoglobin subunit beta NP_000509.1:p.His144fs H (His) > P (Pro) 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: delT (allele ID: 30384 )
ClinVar Accession Disease Names Clinical Significance
RCV000016588.4 HEMOGLOBIN SAVERNE Other
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 T= delT Note
GRCh38.p12 chr 11 NC_000011.10:g.5225611= NC_000011.10:g.5225611del
GRCh37.p13 chr 11 NC_000011.9:g.5246841= NC_000011.9:g.5246841del
HBB region RefSeqGene NG_000007.3:g.72005= NG_000007.3:g.72005del
HBB RefSeqGene NG_059281.1:g.6461= NG_059281.1:g.6461del
HBB transcript NM_000518.5:c.431= NM_000518.5:c.431del
HBB transcript NM_000518.4:c.431= NM_000518.4:c.431del
LOC107133510 genomic region NG_046672.1:g.3546= NG_046672.1:g.3546del
LOC110006319 genomic region NG_053049.1:g.1932= NG_053049.1:g.1932del
hemoglobin subunit beta NP_000509.1:p.His144= NP_000509.1:p.His144fs
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 SubSNP, 1 ClinVar submissions
No Submitter Submission ID Date (Build)
1 MILLER_NIDDK ss49851162 Dec 14, 2012 (137)
2 HBVAR ss79090080 Oct 02, 2012 (137)
3 ClinVar RCV000016588.4 Oct 12, 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
RCV000016588.4, ss49851162, ss79090080 NC_000011.10:5225610:T: NC_000011.10:5225610:T: (self)
Help

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

2 citations for rs63749858
PMID Title Author Year Journal
2283297 A new beta-thalassemia mutation produced by a single nucleotide substitution in the conserved dinucleotide sequence of the IVS-I consensus acceptor site (AG----AA). Deidda G et al. 1990 Hemoglobin
3170236 Hemoglobin Saverne: a new variant with elongated beta chains: structural and functional properties. Delanoe-Garin J et al. 1988 Hemoglobin

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