NM_000518.5(HBB):c.*56A>G AND not provided

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

Germline classification:: Likely benign (2 submissions)
Last evaluated:: Dec 6, 2020
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:: RCV000588701.5

Allele description

NM_000518.5(HBB):c.*56A>G

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.*56A>G

HGVS:

NC_000011.10:g.5225542T>C
NG_000007.3:g.72074A>G
NG_046672.1:g.3477T>C
NG_053049.1:g.1863T>C
NG_059281.1:g.6530A>G
NM_000518.5:c.*56A>GMANE SELECT
LRG_1232t1:c.*56A>G
LRG_1232:g.6530A>G
NC_000011.9:g.5246772T>C
NM_000518.4:c.*56A>G

Links:

dbSNP: rs537944366

NCBI 1000 Genomes Browser:

rs537944366

Molecular consequence:

NM_000518.5:c.*56A>G - 3 prime UTR variant - [Sequence Ontology: SO:0001624]

Condition(s)

Identifiers:: MedGen: CN517202

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000883983	ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories	criteria provided, single submitter (ARUP Molecular Germline Variant Investigation Process)	Likely benign (May 2, 2018)	germline	clinical testing	Citation Link,
SCV001090565	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely benign (Dec 6, 2020)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000883983

ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories

criteria provided, single submitter

(ARUP Molecular Germline Variant Investigation Process)

Likely benign
(May 2, 2018)

germline

clinical testing

Citation Link,

SCV001090565

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely benign
(Dec 6, 2020)

germline

clinical testing

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

Help

Summary from all submissions

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

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240-242.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories, SCV000883983.1

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

Description

The HBB c.*56A>G variant (rs537944366) has not been reported in the medical literature but is classified as a variant of uncertain significance by one laboratory in ClinVar (Variation ID: 495968) and is observed in the African population at a frequency of 0.15% (13/8730 alleles) in the Genome Aggregation Database. The nucleotide at this position is weakly conserved and computational algorithms (PolyA Signal Miner) predict that the 3â€™ UTR variant has no impact on the transcript. Based on the above information, the variant is considered likely benign.

#	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 Invitae, SCV001090565.3

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

Last Updated: Jun 15, 2021

ClinVar

Relating variation to medicine