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NM_000518.5(HBB):c.59A>G (p.Asn20Ser)

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Interpretation:
Pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
7 (Most recent: Aug 5, 2019)
Last evaluated:
May 2, 2019
Accession:
VCV000015258.4
Variation ID:
15258
Description:
single nucleotide variant
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NM_000518.5(HBB):c.59A>G (p.Asn20Ser)

Allele ID
30297
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
11p15.4
Genomic location
11: 5226963 (GRCh38) GRCh38 UCSC
11: 5248193 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000011.10:g.5226963T>C
NC_000011.9:g.5248193T>C
NG_000007.3:g.70653A>G
... more HGVS
Protein change
N20S
Other names
19A>G
N19S
Canonical SPDI
NC_000011.10:5226962:T:C
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
-
Links
ClinGen: CA125015
UniProtKB: P68871#VAR_002888
OMIM: 141900.0168
dbSNP: rs33972047
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Pathogenic 2 criteria provided, single submitter Mar 20, 2017 RCV000020338.2
Pathogenic 1 criteria provided, single submitter Jun 30, 2017 RCV000508637.1
Pathogenic 1 criteria provided, single submitter May 2, 2019 RCV001000121.2
HEMOGLOBIN MALAY
other 1 no assertion criteria provided Dec 12, 2017 RCV000016479.4
Pathogenic 1 no assertion criteria provided May 1, 1989 RCV000016480.28
Pathogenic 1 no assertion criteria provided May 1, 1989 RCV000016481.28
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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
Pathogenic
(May 02, 2019)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories
Accession: SCV001156560.1
Submitted: (Aug 05, 2019)
Evidence details
Comment:
The Hb Malay variant (HBB: c.59A>G; p.Asn20Ser, also known as Asn19Ser when numbered from the mature protein; rs33972047) is reported in the literature in numerous … (more)
Pathogenic
(Jun 30, 2017)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Quest Diagnostics Nichols Institute San Juan Capistrano
Accession: SCV000605846.1
Submitted: (Aug 01, 2017)
Evidence details
Publications
PubMed (7)
Pathogenic
(Mar 20, 2017)
criteria provided, single submitter
Method: clinical testing
beta Thalassemia
Allele origin: germline
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV000697141.1
Submitted: (Jan 25, 2018)
Evidence details
Publications
PubMed (3)
Comment:
Variant summary: The HBB c.59A>G (p.Asn20Ser) variant involves the alteration of a conserved nucleotide. 3/4 in silico tools predict a benign outcome for this variant … (more)
other
(Dec 12, 2017)
no assertion criteria provided
Method: literature only
HEMOGLOBIN MALAY
Allele origin: germline
OMIM
Accession: SCV000036747.4
Submitted: (Jul 20, 2016)
Evidence details
Publications
PubMed (1)
Pathogenic
(May 01, 1989)
no assertion criteria provided
Method: literature only
BETA-PLUS-THALASSEMIA
Allele origin: germline
OMIM
Accession: SCV000036748.2
Submitted: (Dec 30, 2010)
Evidence details
Publications
PubMed (1)
Pathogenic
(May 01, 1989)
no assertion criteria provided
Method: literature only
BETA-MALAY-THALASSEMIA
Allele origin: germline
OMIM
Accession: SCV000036749.2
Submitted: (Dec 30, 2010)
Evidence details
Publications
PubMed (1)
Pathogenic
(May 14, 2015)
no assertion criteria provided
Method: literature only
beta Thalassemia
Allele origin: germline
GeneReviews
Accession: SCV000040714.2
Submitted: (May 14, 2015)
Evidence details
Other databases
https://www.ncbi.nlm.nih.gov/boo…

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
Beta-Thalassemia Origa R - 2021 PMID: 20301599
Molecular Scanning of β-Thalassemia in the Southern Region of Central Java, Indonesia; a Step Towards a Local Prevention Program. Rujito L Hemoglobin 2015 PMID: 26291967
Transfusion-dependent thalassemia in Northern Sarawak: a molecular study to identify different genotypes in the multi-ethnic groups and the importance of genomic sequencing in unstudied populations. Tan JA Public health genomics 2015 PMID: 25412720
Molecular study and genotype/phenotype correlation of β Thalassemia in Malaysia. Sivalingam M International journal of laboratory hematology 2012 PMID: 22335963
Impact of single nucleotide polymorphisms in HBB gene causing haemoglobinopathies: in silico analysis. George Priya Doss C New biotechnology 2009 PMID: 19429541
beta-thalassemia intermedia caused by compound heterozygosity for Hb Malay (beta codon 19 AAC-->AGC; asn-->Ser) and codons 41/42 (-CTTT) beta(0)-thalassemia mutation. Ma SK American journal of hematology 2000 PMID: 10861818
The molecular basis of beta-thalassemia in Thailand: application to prenatal diagnosis. Thein SL American journal of human genetics 1990 PMID: 2393018
Abnormal processing of beta-Malay globin RNA. Gonzalez-Redondo JM Biochemical and biophysical research communications 1989 PMID: 2775294
Molecular characterization of beta-globin gene mutations in Malay patients with Hb E-beta-thalassaemia and thalassaemia major. Yang KG British journal of haematology 1989 PMID: 2736244
https://www.ncbi.nlm.nih.gov/books/NBK1426/ - - - -

Text-mined citations for rs33972047...

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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 11, 2021