ClinVar Genomic variation as it relates to human health
NM_000518.5(HBB):c.59A>G (p.Asn20Ser)
The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.
Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.
No data submitted for somatic clinical impact
No data submitted for oncogenicity
Variant Details
- Identifiers
-
NM_000518.5(HBB):c.59A>G (p.Asn20Ser)
Variation ID: 15258 Accession: VCV000015258.22
- Type and length
-
single nucleotide variant, 1 bp
- Location
-
Cytogenetic: 11p15.4 11: 5226963 (GRCh38) [ NCBI UCSC ] 11: 5248193 (GRCh37) [ NCBI UCSC ]
- Timeline in ClinVar
-
First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.
Last submission Help The date of the most recent submission for each type of classification for this variant.
Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline Mar 22, 2017 Feb 14, 2024 Aug 25, 2021 - HGVS
-
Nucleotide Protein Molecular
consequenceNM_000518.5:c.59A>G MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000509.1:p.Asn20Ser missense NC_000011.10:g.5226963T>C NC_000011.9:g.5248193T>C NG_000007.3:g.70653A>G NG_042296.1:g.494T>C NG_046672.1:g.4898T>C NG_059281.1:g.5109A>G LRG_1232:g.5109A>G LRG_1232t1:c.59A>G LRG_1232p1:p.Asn20Ser P68871:p.Asn20Ser - Protein change
- N20S
- Other names
-
N19S
19A>G
- Canonical SPDI
- NC_000011.10:5226962:T:C
-
Functional
consequence HelpThe effect of the variant on RNA or protein function, based on experimental evidence from submitters.
- -
-
Global minor allele
frequency (GMAF) HelpThe global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.
- -
-
Allele frequency
Help
The frequency of the allele represented by this VCV record.
- -
- Links
Genes
Gene | OMIM | ClinGen Gene Dosage Sensitivity Curation |
Variation Viewer
Help
Links to Variation Viewer, a genome browser to view variation data from NCBI databases. |
Related variants | ||
---|---|---|---|---|---|---|
HI score
Help
The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
TS score
Help
The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
Within gene
Help
The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants. |
All
Help
The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene. |
|||
HBB | - | - |
GRCh38 GRCh37 |
22 | 1834 | |
LOC106099062 | - | - | - | GRCh38 | - | 862 |
LOC107133510 | - | - | - | GRCh38 | - | 1784 |
Conditions - Germline
Condition
Help
The condition for this variant-condition (RCV) record in ClinVar. |
Classification
Help
The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions) |
Review status
Help
The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. |
Last evaluated
Help
The most recent date that a submitter evaluated this variant for the condition. |
Variation/condition record
Help
The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page. |
---|---|---|---|---|
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 | |
Pathogenic (3) |
criteria provided, single submitter
|
Mar 20, 2017 | RCV000020338.6 | |
Pathogenic (2) |
criteria provided, multiple submitters, no conflicts
|
Aug 25, 2021 | RCV000508637.10 | |
Pathogenic (1) |
criteria provided, single submitter
|
May 2, 2019 | RCV001000121.8 |
Submissions - Germline
Classification
Help
The submitted germline classification for each SCV record. (Last evaluated) |
Review status
Help
Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria) |
Condition
Help
The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant. |
Submitter
Help
The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar. |
More information
Help
This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter. |
|
---|---|---|---|---|---|
Pathogenic
(May 02, 2019)
|
criteria provided, single submitter
Method: clinical testing
|
not specified
Affected status: unknown
Allele origin:
germline
|
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories
Accession: SCV001156560.1
First in ClinVar: Feb 10, 2020 Last updated: Feb 10, 2020 |
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)
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 individuals affected with beta-thalassemia intermedia, either in the homozygous state or in trans to another pathogenic variant (Amran 2017, Ma 2000, Yang 1989, HbVar and references therein). This variant has been reported to segregate with disease in a family and has also been reported in heterozygous individuals with microcytosis and hypochromia (Amran 2017, Yan 1989). This variant is absent from general population databases (Exome Variant Server, Genome Aggregation Database), indicating it is not a common polymorphism. The asparagine at codon 20 is highly conserved, but computational analyses (SIFT: damaging, PolyPhen-2: benign) predict conflicting effects of this variant on protein structure/function. However, computational analyses (Alamut v.2.11) predict that this variant impacts splicing by creating a novel cryptic donor splice site. Based on available information, the Hb Malay variant is considered to be pathogenic. References: HbVar link to Hb Malay: http://globin.bx.psu.edu/cgi-bin/hbvar/query_vars3?mode=output&display_format=page&i=256 Amran HS et al. Case Series of Homozygous and Compound Heterozygosity of Hb Malay, the Diagnostic Features and Transfusion Requirements. J Biomed Clin Sci. 2017 Dec;2(2)23-25. Ma SK et al. 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. Am J Hematol. 2000 Jul;64(3):206-9. Yang KG et al. Molecular characterization of beta-globin gene mutations in Malay patients with Hb E-beta-thalassaemia and thalassaemia major. Br J Haematol. 1989 May;72(1):73-80. (less)
|
|
Pathogenic
(Mar 20, 2017)
|
criteria provided, single submitter
Method: clinical testing
|
beta Thalassemia
Affected status: unknown
Allele origin:
germline
|
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV000697141.1
First in ClinVar: Mar 22, 2017 Last updated: Mar 22, 2017 |
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)
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 (SNPs&GO not captured due to low reliability index). 5/5 splice prediction tools predict that this variant strengthens a cryptic 5' splicing donor site and affects normal splicing. This prediction has been confirmed by at least one functional study (Gonzalez-Redondo_1989). This variant has been found in multiple patients with beta thalassemia (Yang_1989 and Rujito_2015) and is absent in 121362 control chromosomes. In addition, multiple reputable databases classified this variant as pathogenic. Taken together, this variant is classified as pathogenic. (less)
|
|
Pathogenic
(Aug 25, 2021)
|
criteria provided, single submitter
Method: clinical testing
|
not provided
Affected status: unknown
Allele origin:
unknown
|
Quest Diagnostics Nichols Institute San Juan Capistrano
Accession: SCV000605846.4
First in ClinVar: Sep 30, 2017 Last updated: Jan 06, 2024 |
Comment:
The HBB c.59A>G (p.Asn20Ser) pathogenic variant, also known as Hb Malay, is associated with beta (+)-thalassemia. Individuals heterozygous for Hb Malay have mild microcytosis and … (more)
The HBB c.59A>G (p.Asn20Ser) pathogenic variant, also known as Hb Malay, is associated with beta (+)-thalassemia. Individuals heterozygous for Hb Malay have mild microcytosis and hypochromia while homozygous individuals are affected with thalassemia intermedia (PMID: 10861818 (2000), 22335963 (2012), 29695942 (2018)). In addition, this variant has been shown to result in abnormal HBB mRNA splicing (PMID: 2775294 (1989)). (less)
|
|
Pathogenic
(Aug 21, 2021)
|
criteria provided, single submitter
Method: clinical testing
|
not provided
Affected status: unknown
Allele origin:
germline
|
Labcorp Genetics (formerly Invitae), Labcorp
Accession: SCV002140042.3
First in ClinVar: Mar 28, 2022 Last updated: Feb 14, 2024 |
Comment:
This sequence change replaces asparagine with serine at codon 20 of the HBB protein (p.Asn20Ser). The asparagine residue is moderately conserved and there is a … (more)
This sequence change replaces asparagine with serine at codon 20 of the HBB protein (p.Asn20Ser). The asparagine residue is moderately conserved and there is a small physicochemical difference between asparagine and serine. RNA analysis indicates that this missense change induces altered splicing and may result in an absent or disrupted protein product. This variant is not present in population databases (ExAC no frequency). This missense change has been observed in individuals with autosomal recessive beta-thalassemia (PMID: 2736244, 10861818, 25412720). It has also been observed to segregate with disease in related individuals. This variant is also known as CD19AG or Hb Malay. ClinVar contains an entry for this variant (Variation ID: 15258). Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated. Studies have shown that this missense change results in the use of an alternative splice site and introduces a premature termination codon (PMID: 2775294). The resulting mRNA is expected to undergo nonsense-mediated decay. For these reasons, this variant has been classified as Pathogenic. (less)
|
|
Pathogenic
(May 01, 1989)
|
no assertion criteria provided
Method: literature only
|
BETA-PLUS-THALASSEMIA
Affected status: not provided
Allele origin:
germline
|
OMIM
Accession: SCV000036748.2
First in ClinVar: Apr 04, 2013 Last updated: May 09, 2018 |
Comment on evidence:
Yang et al. (1989) found an A-to-G change in codon 19 resulting in beta-plus-thalassemia (613985) in a Malaysian.
|
|
Pathogenic
(May 01, 1989)
|
no assertion criteria provided
Method: literature only
|
BETA-MALAY-THALASSEMIA
Affected status: not provided
Allele origin:
germline
|
OMIM
Accession: SCV000036749.2
First in ClinVar: Apr 04, 2013 Last updated: May 09, 2018 |
Comment on evidence:
Yang et al. (1989) found an A-to-G change in codon 19 resulting in beta-plus-thalassemia (613985) in a Malaysian.
|
|
other
(Dec 12, 2017)
|
no assertion criteria provided
Method: literature only
|
HEMOGLOBIN MALAY
Affected status: not provided
Allele origin:
germline
|
OMIM
Accession: SCV000036747.4
First in ClinVar: Apr 04, 2013 Last updated: Mar 25, 2018 |
Comment on evidence:
Yang et al. (1989) found an A-to-G change in codon 19 resulting in beta-plus-thalassemia (613985) in a Malaysian.
|
|
Pathogenic
(Mar 17, 2017)
|
no assertion criteria provided
Method: clinical testing
|
Beta thalassemia
Affected status: unknown
Allele origin:
germline
|
Natera, Inc.
Accession: SCV002091598.1
First in ClinVar: Apr 23, 2022 Last updated: Apr 23, 2022 |
|
|
not provided
(-)
|
no classification provided
Method: literature only
|
beta Thalassemia
Affected status: unknown
Allele origin:
germline
|
GeneReviews
Accession: SCV000040714.4
First in ClinVar: Apr 04, 2013 Last updated: Oct 01, 2022 |
|
Germline Functional Evidence
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 germline classification of this variant
HelpTitle | Author | Journal | Year | Link |
---|---|---|---|---|
Beta-Thalassemia. | Adam MP | - | 2024 | PMID: 20301599 |
Molecular Spectrum of β-Thalassemia Mutations in Central to Eastern Thailand. | Panichchob P | Hemoglobin | 2021 | PMID: 33966551 |
Borderline hemoglobin A(2) levels in northern Thai population: HBB genotypes and effects of coinherited alpha-thalassemia. | Chaweephisal P | Blood cells, molecules & diseases | 2019 | PMID: 30309760 |
Genotype-phenotype correlation among beta-thalassemia and beta-thalassemia/HbE disease in Thai children: predictable clinical spectrum using genotypic analysis. | Traivaree C | Journal of blood medicine | 2018 | PMID: 29695942 |
Non-Invasive DNA Sampling for Molecular Analysis of Beta-Thalassemia: Amiable Alternative Sampling Methods with Accurate Results for Pediatric Patients. | Abd Rahim MR | Clinical laboratory | 2015 | PMID: 26554253 |
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 |
Comprehensive and efficient HBB mutation analysis for detection of beta-hemoglobinopathies in a pan-ethnic population. | Chan OT | American journal of clinical pathology | 2010 | PMID: 20395516 |
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 |
click to load more click to collapse |
Text-mined citations for rs33972047 ...
HelpRecord last updated Sep 29, 2024
This date represents the last time this VCV record was updated. The update may be due to an update to one of the included submitted records (SCVs), or due to an update that ClinVar made to the variant such as adding HGVS expressions or a rs number. So this date may be different from the date of the “most recent submission” reported at the top of this page.