NM_000518.4(HBB):c.316-106C>G AND beta Thalassemia

This record was updated by the submitter. Please see the current version.

Germline classification:: Pathogenic (3 submissions)
Last evaluated:: Jul 5, 2016
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV000029978.3

Allele description

NM_000518.4(HBB):c.316-106C>G

Gene:

HBB:hemoglobin subunit beta [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

11p15.4

Genomic location:

Preferred name:

NM_000518.4(HBB):c.316-106C>G

Other names:

IVS2-745C>G

HGVS:

NC_000011.10:g.5225832G>C
NG_000007.3:g.71784C>G
NM_000518.4:c.316-106C>G
NC_000011.9:g.5247062G>C

Nucleotide change:

IVS2, C-G, +745

Links:

OMIM: 141900.0367; dbSNP: rs34690599

NCBI 1000 Genomes Browser:

rs34690599

Molecular consequence:

NM_000518.4:c.316-106C>G - intron variant - [Sequence Ontology: SO:0001627]

Observations:

Condition(s)

Name:: beta Thalassemia (BTHAL)
Identifiers:: MedGen: C0005283; Orphanet: 848; OMIM: 613985

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000040709	GeneReviews	no assertion criteria provided	Pathogenic (May 14, 2015)	germline	literature only	Citation Link,
SCV000052633	Laboratory Corporation of America	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	pathogenic (Aug 18, 2011)	germline	curation, clinical testing	PubMed (25) [See all records that cite these PMIDs] 8330981, 3422218, 1634236, 6583702, 1390250, 18603555, 2298457, 9401495, 9048934, 2577233, 9140720, 21119755, 16311287, 12764548, 20704537, 17331080, 2200760, 1917531, 2446680, 20437613, 15108284, 6280057, 6188062, 11857746, 19254853 Citation Link,
SCV000331532	EGL Genetic Diagnostics,Eurofins Clinical Diagnostics	criteria provided, single submitter (EGL Classification Definitions)	Pathogenic (Jul 5, 2016)	germline	clinical testing	PubMed (1) [See all records that cite this PMID] Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000040709

GeneReviews

no assertion criteria provided

Pathogenic
(May 14, 2015)

germline

literature only

Citation Link,

SCV000052633

Laboratory Corporation of America

criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)

pathogenic
(Aug 18, 2011)

germline

curation, clinical testing

PubMed (25)
[See all records that cite these PMIDs]

Citation Link,

SCV000331532

EGL Genetic Diagnostics,Eurofins Clinical Diagnostics

criteria provided, single submitter

(EGL Classification Definitions)

Pathogenic
(Jul 5, 2016)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	27	not provided	not provided	17	not provided	literature only
not provided	germline	unknown	2	not provided	not provided	not provided	not provided	clinical testing
Mediterranean	germline	unknown	not provided	not provided	not provided	not provided	not provided	literature only

Citations

PubMed

IVS-I-1 (G-->C) in combination with -42 (C-->G) in the promoter region of the beta-globin gene in patients from Tajikistan.

Fedorov AN, Nasyrova FYu, Smirnova EA, Bocharova TN, Limborska SA.

Hemoglobin. 1993 Jun;17(3):275-8. No abstract available.

PubMed [citation]

PMID:: 8330981

The peculiar spectrum of beta-thalassemia genes in Tunisia.

Chibani J, Vidaud M, Duquesnoy P, Bergé-Lefranc JL, Pirastu M, Ellouze F, Rosa J, Goossens M.

Hum Genet. 1988 Feb;78(2):190-2.

PubMed [citation]

PMID:: 3422218

See all PubMed Citations (26)

Details of each submission

From GeneReviews, SCV000040709.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	Mediterranean	not provided	not provided	not provided	literature only	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Laboratory Corporation of America, SCV000052633.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	20	not provided	not provided	curation	PubMed (25)
2	not provided	7	not provided	not provided	curation	PubMed (25)
3	not provided	not provided	not provided	not provided	clinical testing	PubMed (25)

Description

"Common DV in Mediterranean populations; The variant is reported to have an allele frequency of 6.4% in Egypt; numbers are fabricated here to saturate the tbGP score since this is a common DV.": PubMed [ID: 8330981]
"Seven patients compound heterozygous for the variant and a BTHAL variant (DV) are clinically diagnosed with BTHAL; controls not tested.": PubMed [ID: 2200760]

Description

Converted during submission to Pathogenic.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	10	not provided	not provided		20	not provided	not provided	not provided
2	germline	yes	7	not provided	not provided		7	not provided	not provided	not provided
3	germline	unknown	not provided	Blood	assert pathogenicity		not provided	not provided	not provided	See 3

Co-occurrences

#	Zygosity	Alleles	Number of Observations
3	SingleHeterozygote	HBB:c.9T>C, HBB:c.316-185C>T, HBB:c.315+16G>C, HBB:c.-31C>T	1

From EGL Genetic Diagnostics,Eurofins Clinical Diagnostics, SCV000331532.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	1	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		1	not provided	not provided	not provided

Last Updated: Dec 26, 2017

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