Variant rs63751208 details in Genebe, Genetics Data Aggregator

Genes affected

HBB (HGNC:4827): (hemoglobin subunit beta) The alpha (HBA) and beta (HBB) loci determine the structure of the 2 types of polypeptide chains in adult hemoglobin, Hb A. The normal adult hemoglobin tetramer consists of two alpha chains and two beta chains. Mutant beta globin causes sickle cell anemia. Absence of beta chain causes beta-zero-thalassemia. Reduced amounts of detectable beta globin causes beta-plus-thalassemia. The order of the genes in the beta-globin cluster is 5'-epsilon -- gamma-G -- gamma-A -- delta -- beta--3'. [provided by RefSeq, Jul 2008]

HBB links:

ACMG classification

Classification made for transcript

Verdict is Likely_pathogenic. Variant got 9 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

PP5

Variant 11-5227172-G-A is Pathogenic according to our data. Variant chr11-5227172-G-A is described in ClinVar as [Pathogenic]. Clinvar id is 15461.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-5227172-G-A is described in Lovd as [Pathogenic]. Variant chr11-5227172-G-A is described in Lovd as [Pathogenic]. Variant chr11-5227172-G-A is described in Lovd as [Likely_pathogenic].

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.34). . Strength limited to SUPPORTING due to the PP5.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	Protein	UniProt
HBB	ENST00000647020.1 link	c.-151C>T	5_prime_UTR_premature_start_codon_gain_variant	Exon 1 of 3		ENSP00000494175.1	P68871
HBB	ENST00000647020.1 link	c.-151C>T	5_prime_UTR_variant	Exon 1 of 3		ENSP00000494175.1	P68871
HBB	ENST00000380315.2 link	c.-18-133C>T	intron_variant	Intron 2 of 3	5	ENSP00000369671.2	F8W6P5

Frequencies

GnomAD3 genomes

AF:

0.0000657

AC:

AN:

152190

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000147

Gnomad OTH

AF:

0.00

GnomAD4 exome

AF:

0.000104

AC:

AN:

537340

Hom.:

Cov.:

AF XY:

0.000124

AC XY:

AN XY:

290572

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.0000292

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000117

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.000129

Gnomad4 OTH exome

AF:

0.000135

GnomAD4 genome

AF:

0.0000657

AC:

AN:

152190

Hom.:

Cov.:

AF XY:

0.0000672

AC XY:

AN XY:

74352

show subpopulations

Gnomad4 AFR

AF:

0.00

Gnomad4 AMR

AF:

0.00

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000147

Gnomad4 OTH

AF:

0.00

Bravo

AF:

0.0000567

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:14Uncertain:1Other:1

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

beta Thalassemia

Pathogenic:5Other:1

Pathogenic, no assertion criteria provided	clinical testing	Molecular Genetics Laboratory, BC Children's and BC Women's Hospitals	Sep 11, 2023	- -
not provided, no classification provided	literature only	GeneReviews	-	- -
Pathogenic, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Nov 03, 2022	The c.-151C>T variant in HBB, also known as -101C>T, has been reported in the compound heterozygous state with a severe beta thalassemia variant in numerous individuals with a mild form of thalassemia intermedia. It is the most common silent beta-thalassemia variant among individuals of Mediterranean descent (Gonzalez-Redondo 1989 PMID: 2713503, Ristaldi 1990 PMID: 2346726, Rund 1997 PMID: 8980256, HbVar, Maragoudaki 1999 PMID: 10606872). It has also been reported in ClinVar (Variation ID 15461) and has been identified in 10/68034 European chromosomes by gnomAD (https://gnomad.broadinstitute.org/). This variant occurs in the beta-globin promoter, and in vitro functional studies support an impact on promoter activity (Gonzalez-Redondo 1989 PMID: 2713503). In summary, this variant meets criteria to be classified as pathogenic for autosomal recessive beta thalassemia. ACMG/AMP Criteria applied: PM2_Supporting, PS4, PM1. -
Pathogenic, criteria provided, single submitter	literature only	Counsyl	Apr 17, 2014	- -
Pathogenic, no assertion criteria provided	clinical testing	Natera, Inc.	Mar 17, 2017	- -
Pathogenic, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Aug 07, 2017	Variant summary: c.-151C>T affects a non-conserved nucleotide in the promoter of HBB gene. Mutation Taster predicts a damaging outcome for this variant. This prediction was confirmed by a CAT promoter activity assay showing that this variant decreased promoter activity by 70% (Gonzalez-Redondo_1989). This variant was found in 1/31016 control chromosomes at a frequency of 0.0000322, which does not exceed the estimated maximal expected allele frequency of a pathogenic HBB variant (0.0111803). This variant is a well-known pathogenic HBB variant and has been reported in more than thirty unrelated patients with b-thalassemia intermedia. In addition, multiple clinical laboratories/reputable databases classified this variant as pathogenic. Taken together, this variant was classified as pathogenic. -

not provided

Pathogenic:5

Pathogenic, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Mar 17, 2024	This variant occurs in a non-coding region of the HBB gene. It does not change the encoded amino acid sequence of the HBB protein. This variant is present in population databases (rs63751208, gnomAD 0.007%). This variant has been observed in individuals with HBB-related conditions, usually co-occurring with another severe beta-thalassemia variant (PMID: 2001456, 2713503, 10606872). It has also been observed to segregate with disease in related individuals. Of note, one homozygous individual was reported with beta-thalassemia intermedia (PMID: 30820323). This variant is also known as -101C>T. Studies have shown that this variant alters HBB gene expression (PMID: 2713503). For these reasons, this variant has been classified as Pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Sep 15, 2022	Published functional studies demonstrate a significant loss of function (Gonzalez-Redondo et al., 1989); Not observed at significant frequency in large population cohorts (gnomAD); Reported as the most common silent beta-thalassemia variant among individuals of Mediterranean background (Maragoudaki et al., 1999); This variant is associated with the following publications: (PMID: 2001456, 7683931, 2346726, 25910213, 2713503, 7909640, 26202972, 28385923, 31395865, 34426522, 10606872) -
Pathogenic, criteria provided, single submitter	clinical testing	Quest Diagnostics Nichols Institute San Juan Capistrano	Aug 22, 2024	The HBB c.-151C>T variant (also known as -101C>T) has been reported in the homozygous and compound heterozygous state in individuals with beta-thalassemia intermedia (PMID: 30820323 (2019), 10606872 (1999), 2346726 (1990)). A functional study indicate this variant results in reduced HBB promoter activity (PMID: 2713503 (1989)). The frequency of this variant in the general population, 0.000032 (1/31400 chromosomes (Genome Aggregation Database, http://gnomad.broadinstitute.org)), is uninformative in the assessment of its pathogenicity. Based on the available information, this variant is classified as pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	Apr 03, 2023	The HBB c.-151C>T variant (rs63751208, HbVar ID: 649), also known as -101C>T, is associated with silent beta thalassemia in heterozygous carriers and has been described in individuals with a mild form of thalassemia intermedia who were compound heterozygous with a severe beta thalassemia variant (Gonzalez-Redondo 1989, Ristaldi 1990, Rund 1997, see HbVar and references therein). This variant is also reported in ClinVar (Variation ID: 15461). It is only observed on one allele in the Genome Aggregation Database, indicating it is not a common polymorphism. This variant is located in a conserved region of the beta globin gene promoter and is considered to be pathogenic. References: Link to HbVar database: https://globin.bx.psu.edu/hbvar/menu.html Gonzalez-Redondo JM et al. A C----T substitution at nt--101 in a conserved DNA sequence of the promotor region of the beta-globin gene is associated with "silent" beta-thalassemia. Blood. 1989 May 1;73(6):1705-11. PMID: 2713503 Ristaldi MS et al. The C-T substitution in the distal CACCC box of the beta-globin gene promoter is a common cause of silent beta thalassaemia in the Italian population. Br J Haematol. 1990 Apr;74(4):480-6. PMID: 2346726 Rund D et al. Genetic analysis of beta-thalassemia intermedia in Israel: diversity of mechanisms and unpredictability of phenotype. Am J Hematol. 1997 Jan;54(1):16-22. PMID: 8980256 -
Pathogenic, criteria provided, single submitter	clinical testing	Revvity Omics, Revvity	Jun 18, 2021	- -

Beta-thalassemia HBB/LCRB

Pathogenic:1

Pathogenic, criteria provided, single submitter

curation

Laboratory of Medical Genetics, National & Kapodistrian University of Athens

Feb 01, 2024

- -

HBB-related disorder

Pathogenic:1

Pathogenic, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Dec 28, 2023

The HBB c.-151C>T variant is located in the 5' untranslated region. This variant, also referred to as c.-101C>T using legacy nomenclature, is predicted to disrupt the CACCC promoter motif and has been reported to be causative for Beta-Thalassemia in the presence of a second pathogenic allele (Gonzalez-Redondo et al. 1989. PubMed ID: 2713503; Rund et al. 1997. PubMed ID: 8980256; Ristaldi et al. 1999. PubMed ID: 10575515). This variant is reported in 0.0065% of alleles in individuals of European (Non-Finnish) descent in gnomAD. This variant is interpreted as pathogenic. -

Hb SS disease;C0019025:Hereditary persistence of fetal hemoglobin;C0700299:Heinz body anemia;C1840779:METHEMOGLOBINEMIA, BETA TYPE;C1858990:Dominant beta-thalassemia;C1970028:Malaria, susceptibility to;C4693822:Erythrocytosis, familial, 6;CN322236:Beta-thalassemia HBB/LCRB

Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Fulgent Genetics, Fulgent Genetics

Apr 15, 2024

- -

Beta-plus-thalassemia

Pathogenic:1

Pathogenic, no assertion criteria provided

literature only

OMIM

Dec 01, 1999

- -

Malaria, susceptibility to

Uncertain:1

Uncertain significance, flagged submission

clinical testing

Genomic Medicine Center of Excellence, King Faisal Specialist Hospital and Research Centre

Mar 25, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.34

CADD

Benign

DANN

Benign

0.76

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

rs63751208

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

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