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NM_000518.5(HBB):c.93-23T>C

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Interpretation:
Conflicting interpretations of pathogenicity​

Benign(2);Likely benign(1);Uncertain significance(2)

Review status:
criteria provided, conflicting interpretations
Submissions:
6 (Most recent: Jan 7, 2021)
Last evaluated:
Dec 4, 2020
Accession:
VCV000036340.11
Variation ID:
36340
Description:
single nucleotide variant
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NM_000518.5(HBB):c.93-23T>C

Allele ID
45004
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
11p15.4
Genomic location
11: 5226822 (GRCh38) GRCh38 UCSC
11: 5248052 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
LRG_1232:g.5250T>C
LRG_1232t1:c.93-23T>C
NC_000011.10:g.5226822A>G
... more HGVS
Protein change
-
Other names
IVS I-108 T>C
Canonical SPDI
NC_000011.10:5226821:A:G
Functional consequence
-
Global minor allele frequency (GMAF)
0.00639 (G)

Allele frequency
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00539
1000 Genomes Project 0.00639
Trans-Omics for Precision Medicine (TOPMed) 0.00568
The Genome Aggregation Database (gnomAD) 0.00513
The Genome Aggregation Database (gnomAD), exomes 0.00139
Exome Aggregation Consortium (ExAC) 0.00173
The Genome Aggregation Database (gnomAD) 0.00593
Trans-Omics for Precision Medicine (TOPMed) 0.00665
Links
ClinGen: CA342879
dbSNP: rs111851677
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Uncertain significance 3 criteria provided, multiple submitters, no conflicts May 28, 2019 RCV000030010.4
Benign/Likely benign 2 criteria provided, multiple submitters, no conflicts Dec 4, 2020 RCV000860961.4
Benign 1 criteria provided, single submitter Mar 24, 2020 RCV000507701.4
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
HBB - - GRCh38
GRCh37
45 1293
LOC106099062 - - - GRCh38 - 702
LOC107133510 - - - GRCh38 - 1226

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
uncertain
(Aug 18, 2011)
criteria provided, single submitter
Method: clinical testing
Beta Thalassemia
(autosomal unknown)
Allele origin: germline
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV000052665.1
Submitted: (Aug 18, 2011)
Evidence details
Comment:
Converted during submission to Uncertain significance.
Benign
(Mar 24, 2020)
criteria provided, single submitter
Method: clinical testing
none provided
Allele origin: germline
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories
Accession: SCV000603926.3
Submitted: (Dec 11, 2020)
Evidence details
Uncertain significance
(May 28, 2019)
criteria provided, single submitter
Method: clinical testing
beta Thalassemia
Allele origin: unknown
Mendelics
Accession: SCV001138220.1
Submitted: (Oct 22, 2019)
Evidence details
Likely benign
(Nov 18, 2018)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Quest Diagnostics Nichols Institute San Juan Capistrano
Accession: SCV001134241.2
Submitted: (Mar 06, 2020)
Evidence details
Publications
PubMed (4)
Benign
(Dec 04, 2020)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Invitae
Accession: SCV001001151.3
Submitted: (Jan 07, 2021)
Evidence details
Benign
(Nov 25, 2019)
no assertion criteria provided
Method: curation
beta Thalassemia
Allele origin: germline
The ITHANET community portal, The Cyprus Institute of Neurology and Genetics
Accession: SCV001244517.1
Submitted: (Nov 25, 2019)
Evidence details
Publications
PubMed (4)
Other databases
https://ithanet.eu/db/ithagenes?…

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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Title Author Journal Year Link
Phenotypic evaluations of <i>HBB</i>:c.93-23T&gt;C, a nucleotide substitution in the IVS I nt 108 of β-globin gene. Vinciguerra M Journal of clinical pathology 2017 PMID: 28794124
Pathogenic variants for Mendelian and complex traits in exomes of 6,517 European and African Americans: implications for the return of incidental results. Tabor HK American journal of human genetics 2014 PMID: 25087612
Evaluation of the validity of Hb A2 and mean corpuscular haemoglobin action values in antenatal screening for beta thalassaemia carriers in England. Daniel Y British journal of haematology 2014 PMID: 24754789
The molecular heterogeneity of beta-thalassemia in Greece. Boussiou M Blood cells, molecules & diseases 2008 PMID: 18096416
Beta-thalassaemia in Cubans: novel allele increases the genetic diversity at the HBB locus in the Caribbean. Muñiz A American journal of hematology 2000 PMID: 10815781
Characterization of a new polymorphism, IVS-I-108 (T--&gt;C), and a new beta-thalassemia mutation, -27 (A--&gt;T), discovered in the course of a prenatal diagnosis. Badens C Hemoglobin 1999 PMID: 10569722
https://ithanet.eu/db/ithagenes?ithaID=3066 - - - -

Text-mined citations for rs111851677...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Nov 27, 2021