NM_000518.5(HBB):c.-80T>A AND not specified

Clinical significance:Pathogenic (Last evaluated: Oct 5, 2018)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV001000147.2

Allele description [Variation Report for NM_000518.5(HBB):c.-80T>A]

NM_000518.5(HBB):c.-80T>A

Genes:
HBB:hemoglobin subunit beta [Gene - OMIM - HGNC]
LOC106099062:HBB recombination region [Gene]
LOC107133510:origin of replication at HBB [Gene]
Variant type:
single nucleotide variant
Cytogenetic location:
11p15.4
Genomic location:
Preferred name:
NM_000518.5(HBB):c.-80T>A
Other names:
-30T>A; -30 (T>A)
HGVS:
  • NC_000011.10:g.5227101A>T
  • NG_000007.3:g.70515T>A
  • NG_042296.1:g.632A>T
  • NG_046672.1:g.5036A>T
  • NG_059281.1:g.4971T>A
  • NM_000518.4(HBB):c.-80T>A
  • HBB:c.-80T>A
  • LRG_1232:g.4971T>A
  • NC_000011.9:g.5248331A>T
  • NM_000518.4(HBB):c.-80T>A
  • NM_000518.4:c.-80T>A
Nucleotide change:
-30T-A, PROMOTER
Links:
Genetic Testing Registry (GTR): GTR000500319; HBVAR: 765; OMIM: 141900.0377; dbSNP: rs33980857
NCBI 1000 Genomes Browser:
rs33980857

Condition(s)

Synonyms:
AllHighlyPenetrant
Identifiers:
MedGen: CN169374

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001156632ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratoriescriteria provided, single submitter
Pathogenic
(Oct 5, 2018)
germlineclinical testing

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories, SCV001156632.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The HBB c.-80T>A variant, also known as -30 (T>A), is published in the medical literature in individuals with beta thalassemia intermedia when in the homozygous state and in individuals with a deletion on the opposite chromosome (see link to HbVar database, Fei 1988, Griffon 2010). The variant is listed in the ClinVar database (Variation ID: 15467) and the dbSNP variant database (rs33980857). This variant occurs in the conserved promoter region (Giardine 2011) and is predicted to affect transcription factor binding , thus reducing but not completely abrogating the amount of message produced from that chromosome (beta +). Considering available information, this variant is classified as pathogenic. References: Link to variant in HbVar database: http://globin.bx.psu.edu/cgi-bin/hbvar/query_vars3?mode=output&display_format=page&i=765&.cgifields=histD Fei YJ et al. Beta-thalassemia due to a T----A mutation within the ATA box. Biochem Biophys Res Commun. 1988 Jun 16;153(2):741-7. Giardine B et al. Systematic documentation and analysis of human genetic variation in hemoglobinopathies using the microattribution approach. Nat Genet. 2011 Mar 20;43(4):295-301. Griffon C et al. Severe B-thalassemia intermedia in a compound heterozygous patient for the -30 (T>A) B(+)-thalassemia mutation and the D(0)B(+)-Senegalese deletion. Hemoglobin. 2010;34(5):505-8.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Nov 27, 2021

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