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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 Aliases 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.

rs63749819

Current Build 153

Released July 9, 2019

Organism
Homo sapiens
Position
chr11:5227002 (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
delT=0.00002 (4/251184, GnomAD_exome)
delT=0.00003 (4/125568, TOPMED)
delT=0.00002 (3/121348, ExAC)
Clinical Significance
Reported in ClinVar
Gene : Consequence
HBB : Coding Sequence Variant
Publications
7 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.5227002del
GRCh37.p13 chr 11 NC_000011.9:g.5248232del
HBB region RefSeqGene NG_000007.3:g.70614del
HBB RefSeqGene NG_059281.1:g.5070del
LOC107133510 genomic region NG_046672.1:g.4937del
LOC106099062 genomic region NG_042296.1:g.533del
Gene: HBB, hemoglobin subunit beta (minus strand)
Molecule type Change Amino acid[Codon] SO Term
HBB transcript NM_000518.5:c.20del E [GAG] > G [GG] Coding Sequence Variant
hemoglobin subunit beta NP_000509.1:p.Glu7fs E (Glu) > G (Gly) 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: 30457 )
ClinVar Accession Disease Names Clinical Significance
RCV000016674.29 beta^0^ Thalassemia Pathogenic
RCV000506769.1 not provided Pathogenic
RCV000576555.1 beta Thalassemia 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").

Download
Study Population Group Sample Size Ref Allele Alt Allele
gnomAD - Exomes Global Study-wide 251184 T=0.99998 delT=0.00002
gnomAD - Exomes European Sub 135180 T=0.99998 delT=0.00002
gnomAD - Exomes Asian Sub 48978 T=1.0000 delT=0.0000
gnomAD - Exomes American Sub 34572 T=1.0000 delT=0.0000
gnomAD - Exomes African Sub 16256 T=0.9999 delT=0.0001
gnomAD - Exomes Ashkenazi Jewish Sub 10068 T=1.0000 delT=0.0000
gnomAD - Exomes Other Sub 6130 T=1.000 delT=0.000
TopMed Global Study-wide 125568 T=0.99997 delT=0.00003
ExAC Global Study-wide 121348 T=0.99998 delT=0.00002
ExAC Europe Sub 73352 T=1.0000 delT=0.0000
ExAC Asian Sub 25130 T=1.0000 delT=0.0000
ExAC American Sub 11552 T=1.0000 delT=0.0000
ExAC African Sub 10406 T=0.9999 delT=0.0001
ExAC Other Sub 908 T=1.00 delT=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 T= delT Note
GRCh38.p12 chr 11 NC_000011.10:g.5227002= NC_000011.10:g.5227002del
GRCh37.p13 chr 11 NC_000011.9:g.5248232= NC_000011.9:g.5248232del
HBB region RefSeqGene NG_000007.3:g.70614= NG_000007.3:g.70614del
HBB RefSeqGene NG_059281.1:g.5070= NG_059281.1:g.5070del
HBB transcript NM_000518.5:c.20= NM_000518.5:c.20del
HBB transcript NM_000518.4:c.20= NM_000518.4:c.20del
LOC107133510 genomic region NG_046672.1:g.4937= NG_046672.1:g.4937del
LOC106099062 genomic region NG_042296.1:g.533= NG_042296.1:g.533del
hemoglobin subunit beta NP_000509.1:p.Glu7= NP_000509.1:p.Glu7fs
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#.

5 SubSNP, 3 Frequency, 3 ClinVar submissions
No Submitter Submission ID Date (Build)
1 MILLER_NIDDK ss49851102 Dec 14, 2012 (137)
2 HBVAR ss79090108 Oct 02, 2012 (137)
3 EVA_EXAC ss1711960331 Apr 01, 2015 (144)
4 GNOMAD ss2738739465 Nov 08, 2017 (151)
5 TOPMED ss3135962131 Nov 08, 2017 (151)
6 ExAC NC_000011.9 - 5248232 Oct 12, 2018 (152)
7 gnomAD - Exomes NC_000011.9 - 5248232 Jul 13, 2019 (153)
8 TopMed NC_000011.10 - 5227002 Oct 12, 2018 (152)
9 ClinVar RCV000016674.29 Oct 12, 2018 (152)
10 ClinVar RCV000506769.1 Oct 12, 2018 (152)
11 ClinVar RCV000576555.1 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
466251, 7946311, ss1711960331, ss2738739465 NC_000011.9:5248231:T: NC_000011.10:5227001:T: (self)
RCV000016674.29, RCV000506769.1, RCV000576555.1, 56037335, ss49851102, ss79090108, ss3135962131 NC_000011.10:5227001:T: NC_000011.10:5227001:T: (self)
Help

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

7 citations for rs63749819
PMID Title Author Year Journal
1734721 Molecular characterization of beta-thalassemia in the Sardinian population. Rosatelli MC et al. 1992 American journal of human genetics
2200762 Beta-thalassemia in Bulgaria. Petkov GH et al. 1990 Hemoglobin
2393712 A new mutation at IVS1 nt 2(T----A), in beta-thalassemia from Algeria. Bouhass R et al. 1990 Blood
2458145 Clinical and genetic heterogeneity in black patients with homozygous beta-thalassemia from the southeastern United States. Gonzalez-Redondo JM et al. 1988 Blood
6310991 beta-Thalassemia due to a deletion of the nucleotide which is substituted in the beta S-globin gene. Kazazian HH Jr et al. 1983 American journal of human genetics
8262525 Rapid detection of single nucleotide deletions: application to the beta 6 (-A) mutation of the beta-globin gene and to cystic fibrosis. Romey MC et al. 1993 Human genetics
27351925 Development of a High-Resolution Melting Approach for Scanning Beta Globin Gene Point Mutations in the Greek and Other Mediterranean Populations. Chassanidis C et al. 2016 PloS one

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.post308+0fe9b3b