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rs33971634

Variant summary

Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PVS1PM2PP5_Very_Strong

The NM_000518.5(HBB):c.382C>T(p.Gln128Ter) variant causes a stop gained change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000657 in 152,252 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★★).

Frequency

Genomes: 𝑓 0.0000066 ( 0 hom., cov: 33)

Consequence

HBB
NM_000518.5 stop_gained

Scores

5
1
1

Clinical Significance

Pathogenic criteria provided, multiple submitters, no conflicts P:2

Conservation

PhyloP100: 9.01
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Pathogenic. Variant got 18 ACMG points.

PVS1
Loss of function variant, product does not undergo nonsense mediated mRNA decay. Variant is located in the 3'-most exon, not predicted to undergo nonsense mediated mRNA decay. There are 54 pathogenic variants in the truncated region.
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant 11-5225660-G-A is Pathogenic according to our data. Variant chr11-5225660-G-A is described in ClinVar as [Pathogenic]. Clinvar id is 1705074.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-5225660-G-A is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
HBBNM_000518.5 linkuse as main transcriptc.382C>T p.Gln128Ter stop_gained 3/3 ENST00000335295.4

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
HBBENST00000335295.4 linkuse as main transcriptc.382C>T p.Gln128Ter stop_gained 3/31 NM_000518.5 P1
HBBENST00000647020.1 linkuse as main transcriptc.382C>T p.Gln128Ter stop_gained 3/3 P1
HBBENST00000475226.1 linkuse as main transcriptn.314C>T non_coding_transcript_exon_variant 2/22
HBBENST00000633227.1 linkuse as main transcriptc.*198C>T 3_prime_UTR_variant, NMD_transcript_variant 3/33

Frequencies

GnomAD3 genomes
AF:
0.00000657
AC:
1
AN:
152134
Hom.:
0
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0000655
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:
0.00
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.00000398
AC:
1
AN:
251276
Hom.:
0
AF XY:
0.00000736
AC XY:
1
AN XY:
135810
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.0000289
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
Cov.:
31
GnomAD4 genome
AF:
0.00000657
AC:
1
AN:
152252
Hom.:
0
Cov.:
33
AF XY:
0.0000134
AC XY:
1
AN XY:
74448
show subpopulations
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.0000654
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.00
ExAC
AF:
0.00000824
AC:
1

ClinVar

Significance: Pathogenic
Submissions summary: Pathogenic:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

Dominant beta-thalassemia Pathogenic:1
Pathogenic, criteria provided, single submitterclinical testingWomen's Health and Genetics/Laboratory Corporation of America, LabCorpMar 17, 2023Variant summary: HBB c.382C>T (p.Gln128X, also reported as p.Glu127X) is located in exon 3 (i.e. in the last exon) of the HBB gene. The current variant results in a premature termination codon that is not expected to cause nonsense mediated decay (NMD), but is predicted to cause a C-terminal truncation, removing a part of the 147 amino acid long protein. A truncation downstream of this position has been classified as pathogenic for dominant B-THAL by our laboratory. The variant allele was found at a frequency of 4e-06 in 251276 control chromosomes (gnomAD). c.382C>T has been reported in the literature in multiple individuals affected with considerable variation in phenotype (even within the same famlily), ranging from mild, clinically asymptomatic anemia to severe hemolytic anemia with splenomegaly (e.g. Hall_1991, Van Weel_1999, Prehu_2005), where occasionally the presence of Heinz bodies was also noted. These data indicate that the variant is likely associated with disease. A publication reported experimental evidence and demonstrated that substantial amounts of mutant beta-mRNA were present in individuals carrying the variant, thus demonstrating that the variant does not result in nonsense mediated decay (NMD), suggesting that a truncated protein product can be produced, which might also explain the presence of the occasionally reported Heinz bodies (Hall_1994). No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014. Based on the evidence outlined above, the variant was classified as pathogenic for dominant B-THAL. -
not provided Pathogenic:1
Pathogenic, criteria provided, single submitterclinical testingQuest Diagnostics Nichols Institute San Juan CapistranoJun 14, 2023The HBB c.382C>T (p.Gln128*) variant creates a premature stop codon in the last exon of the beta-globin gene. An RNA study indicates the mutant mRNA transcript is not degraded by nonsense-mediated decay, and is predicted to result in the production of a truncated protein lacking the terminal 20 amino acids of the beta-globin chain (PMID: 8161774 (1994)). This variant is associated with dominant beta-thalassemia in which heterozygous carriers present with varying phenotype, ranging from clinically asymptomatic anemia to thalassemia intermedia (PMIDs: 9450794 (1998), 8161774 (1994), 1958498 (1991)). In addition, this variant has been reported as a de novo variant in a heterozygous individual with microcytic hypochromic hemolytic anemia and splenomegaly (PMID: 10569730 (1999)). Previous names for this variant include Codon 127 C>T. Based on the available information, this variant is classified as pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Pathogenic
0.55
D
BayesDel_noAF
Pathogenic
0.62
Cadd
Pathogenic
45
Dann
Uncertain
1.0
Eigen
Pathogenic
1.1
Eigen_PC
Pathogenic
0.92
FATHMM_MKL
Pathogenic
0.99
D
MutationTaster
Benign
1.0
D
Vest4
0.74
GERP RS
4.7

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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.

Other links and lift over

dbSNP: rs33971634; hg19: chr11-5246890; API