NM_000518.5(HBB):c.316-3C>A AND Beta thalassemia intermedia

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Aug 18, 2011
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

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:: RCV000029987.10

Allele description [Variation Report for NM_000518.5(HBB):c.316-3C>A]

NM_000518.5(HBB):c.316-3C>A

Genes:

LOC110006319:beta-globin gene 3' regulatory region [Gene]
HBB:hemoglobin subunit beta [Gene - OMIM - HGNC]
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.316-3C>A

Other names:

IVS II-848 (C>A)

HGVS:

NC_000011.10:g.5225729G>T
NG_000007.3:g.71887C>A
NG_046672.1:g.3664G>T
NG_053049.1:g.2050G>T
NG_059281.1:g.6343C>A
NM_000518.4(HBB):c.316-3C>A
NM_000518.5:c.316-3C>AMANE SELECT
LRG_1232t1:c.316-3C>A
LRG_1232:g.6343C>A
NC_000011.9:g.5246959G>T
NM_000518.4(HBB):c.316-3C>A
NM_000518.4:c.316-3C>A

Nucleotide change:

IVS2, C-A, -3

Links:

Genetic Testing Registry (GTR): GTR000500319; OMIM: 141900.0361; dbSNP: rs33913413

NCBI 1000 Genomes Browser:

rs33913413

Molecular consequence:

NM_000518.5:c.316-3C>A - intron variant - [Sequence Ontology: SO:0001627]

Observations:

Condition(s)

Name:: Beta thalassemia intermedia (BTHAL-ITMD)
Identifiers:: MONDO: MONDO:0016487; MedGen: C0472767

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000052642	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	pathogenic (Aug 18, 2011)	germline	curation, clinical testing	PubMed (8) [See all records that cite these PMIDs] 1917531, 2200760, 20437613, 11857746, 2920213, 2458145, 9140720, 20704537 Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000052642

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)

pathogenic
(Aug 18, 2011)

germline

curation, clinical testing

PubMed (8)
[See all records that cite these PMIDs]

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	7	not provided	not provided	7	not provided	curation
not provided	germline	unknown	5	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Beta-thalassemia, HB S-beta-thalassemia and sickle cell anemia among Tunisians.

Fattoum S, Guemira F, Oner C, Oner R, Li HW, Kutlar F, Huisman TH.

Hemoglobin. 1991;15(1-2):11-21.

PubMed [citation]

PMID:: 1917531

Beta-thalassemia in Turkey.

Oner R, Altay C, Gurgey A, Aksoy M, Kilinç Y, Stoming TA, Reese AL, Kutlar A, Kutlar F, Huisman TH.

Hemoglobin. 1990;14(1):1-13. Review.

PubMed [citation]

PMID:: 2200760

See all PubMed Citations (8)

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV000052642.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	1	not provided	not provided	curation	PubMed (8)
2	not provided	2	not provided	not provided	curation	PubMed (8)
3	not provided	1	not provided	not provided	curation	PubMed (8)
4	not provided	1	not provided	not provided	curation	PubMed (8)
5	not provided	1	not provided	not provided	curation	PubMed (8)
6	not provided	1	not provided	not provided	curation	PubMed (8)
7	not provided	not provided	not provided	not provided	clinical testing	PubMed (8)
8	not provided	not provided	not provided	not provided	clinical testing	PubMed (8)
9	not provided	not provided	not provided	not provided	clinical testing	PubMed (8)
10	not provided	not provided	not provided	not provided	clinical testing	PubMed (8)
11	not provided	not provided	not provided	not provided	clinical testing	PubMed (8)

Description

"Severe BTHAL; has frameshift on other allele; controls not tested.": PubMed [ID: 2920213]
"BTHAL trait (mild); pt het for this variant; no variant specified for other allele; wife also affected with BTHAL trait and carried variant; controls not tested.": PubMed [ID: 2920213]
"BTHAL Major: other allele had a common 5' UTR DV (-79A>G in GE); controls not tested.": PubMed [ID: 2458145]
"BTHAL cohort; type of BTHAL not specified; other allele variants not specified; controls not tested.": PubMed [ID: 9140720]
"BTHAL cohort; type of BTHAL not specified; other allele variants not specified; controls not tested.": PubMed [ID: 9140720]
"Found as het in Mediterranean BTHAL pt using Thalassochip array technology; controls not tested.": PubMed [ID: 20704537]

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	1	not provided	not provided		1	not provided	not provided	not provided
2	germline	yes	2	not provided	not provided		2	not provided	not provided	not provided
3	germline	yes	1	not provided	not provided		1	not provided	not provided	not provided
4	germline	yes	1	not provided	not provided		1	not provided	not provided	not provided
5	germline	yes	1	not provided	not provided		1	not provided	not provided	not provided
6	germline	yes	1	not provided	not provided		1	not provided	not provided	not provided
7	germline	unknown	not provided	Blood	assert pathogenicity		not provided	not provided	not provided	See 7
8	germline	unknown	not provided	Blood	assert pathogenicity		not provided	not provided	not provided	See 8
9	germline	unknown	not provided	Blood	assert pathogenicity		not provided	not provided	not provided	See 9
10	germline	unknown	not provided	Blood	assert pathogenicity		not provided	not provided	not provided	See 10
11	germline	unknown	not provided	Blood	assert pathogenicity		not provided	not provided	not provided	See 11

Co-occurrences

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

Last Updated: Apr 20, 2025

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