rs35424040

chr11-5226940-C-Achr11-5226940-C-Gchr11-5226940-C-T

Variant summary

Our verdict is Pathogenic. Variant got 14 ACMG points: 14P and 0B. PM1PM2PM5PP5_Very_Strong

The NM_000518.5(HBB):c.82G>T(p.Ala28Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000248 in 1,613,406 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely pathogenic (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A28D) has been classified as Pathogenic.

Frequency

Genomes: 𝑓 0.000020 ( 0 hom., cov: 32)

Exomes 𝑓: 6.8e-7 ( 0 hom. )

Consequence

HBB
NM_000518.5 missense

Scores

Clinical Significance

Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:13O:2

Conservation

PhyloP100: 1.22

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]

HBB links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Pathogenic. Variant got 14 ACMG points.

PM1

In a hotspot region, there are 11 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 3 benign, 17 uncertain in NM_000518.5

PM2

Very rare variant in population databases, with high coverage;

PM5

Other missense variant is known to change same aminoacid residue: Variant chr11-5226939-G-T is described in ClinVar as [Pathogenic]. Clinvar id is 15386.Status of the report is criteria_provided_single_submitter, 1 stars.

PP5

Variant 11-5226940-C-A is Pathogenic according to our data. Variant chr11-5226940-C-A is described in ClinVar as [Likely_pathogenic]. Clinvar id is 15239.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-5226940-C-A is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HBB	NM_000518.5 linkuse as main transcript	c.82G>T	p.Ala28Ser	missense_variant	1/3	ENST00000335295.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HBB	ENST00000335295.4 linkuse as main transcript	c.82G>T	p.Ala28Ser	missense_variant	1/3	1	NM_000518.5	P1

Frequencies

GnomAD3 genomes

AF:

0.0000197

AC:

AN:

152226

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000483

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:

0.0000147

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.0000119

AC:

AN:

251362

Hom.:

AF XY:

0.00000736

AC XY:

AN XY:

135850

show subpopulations

Gnomad AFR exome

AF:

0.0000615

Gnomad AMR exome

AF:

0.00

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:

0.0000176

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

6.84e-7

AC:

AN:

1461180

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

726938

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

9.00e-7

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

AF:

0.0000197

AC:

AN:

152226

Hom.:

Cov.:

AF XY:

0.0000269

AC XY:

AN XY:

74376

show subpopulations

Gnomad4 AFR

AF:

0.0000483

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:

0.0000147

Gnomad4 OTH

AF:

0.00

Alfa

AF:

0.0000694

Hom.:

Bravo

AF:

0.0000189

ExAC

AF:

0.00000824

AC:

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:13Other:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Pathogenic:4

Pathogenic, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	Jun 26, 2023	The Hb Knossos variant (HBB: c.82G>T; p.Ala28Ser, also known as Ala27Ser when numbered from the mature protein, rs35424040, HbVar ID: 281) has been reported in multiple unrelated individuals diagnosed with thalassemia intermedia (Altay 1990, Fessas 1982, Orkin 1984, Sirdah 2013), often found in-trans with other pathogenic HBB variants (Altay 1990, Orkin 1984, Sirdah 2013, HbVar and references therein). This variant is listed in ClinVar (Variation ID: 15239), and found in the general population with an overall allele frequency of 0.001% (3/251362 alleles) in the Genome Aggregation Database. Computational analyses predict that the variant activates a nearby cryptic splice donor upstream of the canonical splice site (Alamut v.2.11). Functional studies detected the presence of aberrant mRNA in cells expressing the variant, with a transcript size that is consistent with utilization of the cryptic splice donor predicted by computational algorithms (Orkin 1984). Based on available information, the Hb Knossos variant is considered to be pathogenic. References: Link to HbVar database: https://globin.bx.psu.edu/hbvar/hbvar.html Altay C et al. Beta-thalassemia intermedia in Turkey. Ann N Y Acad Sci. 1990; 612:81-9. PMID: 2291577 Fessas P et al. 'Silent' beta-thalassaemia caused by a 'silent' beta-chain mutant: the pathogenesis of a syndrome of thalassaemia intermedia. Br J Haematol. 1982; 51(4):577-83. PMID: 7104238 Orkin S et al. Abnormal processing of beta Knossos RNA. Blood. 1984; 64(1):311-3. PMID: 6733281 Sirdah M et al. The spectrum of B-thalassemia mutations in Gaza Strip, Palestine. Blood Cells Mol Dis. 2013; 50(4):247-51. PMID: 23321370 -
Pathogenic, criteria provided, single submitter	clinical testing	Quest Diagnostics Nichols Institute San Juan Capistrano	Jun 23, 2021	The variant found in at least one symptomatic individual. The variant occurs in multiple cases with a lone recessive pathogenic/likely pathogenic variant in the same gene, and several have a phenotype known to be consistent with disease. The variant has been shown to be damaging to protein function(s) relevant to disease mechanism. -
Pathogenic, criteria provided, single submitter	clinical testing	Invitae	Oct 25, 2023	This sequence change replaces alanine, which is neutral and non-polar, with serine, which is neutral and polar, at codon 28 of the HBB protein (p.Ala28Ser). RNA analysis indicates that this missense change induces altered splicing and may result in an absent or disrupted protein product. This variant is present in population databases (rs35424040, gnomAD 0.007%). This missense change has been observed in individual(s) with beta-thalassemia major or intermedia (PMID: 2467892, 6469698, 9223924, 17949282). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. This variant is also known as Hb Knossos, Cd27, and Ala27Ser. ClinVar contains an entry for this variant (Variation ID: 15239). Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Not Available"; PolyPhen-2: "Benign"; Align-GVGD: "Not Available". The serine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. Studies have shown that this missense change results in activation of a cryptic splice site and introduces a premature termination codon (PMID: 6733281). The resulting mRNA is expected to undergo nonsense-mediated decay. For these reasons, this variant has been classified as Pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Mar 24, 2023	Published functional studies demonstrate a damaging effect as RNA transcripts are abnormally processed (Orkin et al., 1984); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 25155404, 19429541, 25087612, 25332589, 3955238, 17949282, 26754299, 31553106, 3942130, 6469698, 28399358, 2467892, 9223924, 30777047, 6733281) -

beta Thalassemia

Pathogenic:3Other:1

Pathogenic, criteria provided, single submitter	clinical testing	Genome-Nilou Lab	Jul 22, 2021	- -
Likely pathogenic, criteria provided, single submitter	literature only	Counsyl	Feb 16, 2015	- -
not provided, no classification provided	literature only	GeneReviews	-	- -
Pathogenic, no assertion criteria provided	curation	The ITHANET community portal, The Cyprus Institute of Neurology and Genetics	Nov 25, 2019	- -

Hemoglobinopathy

Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	May 02, 2018	Variant summary: HBB c.82G>T (p.Ala28Ser) results in a conservative amino acid change located in the Globin domain (IPR000971) of the encoded protein sequence. Three of five in-silico tools predict a damaging effect of the variant on protein function. Although 5/5 computational tools predict no significant impact on normal splicing, all 5 tools predict the presence of a cryptic 5' donor site upstream of the canonical splice site. These predictions are supported by a study that showed the presence of an alternative transcript for c.82G>T (Orkin_1984). The variant allele was found at a frequency of 1.2e-05 in 247346 control chromosomes (gnomAD and publications). This frequency is not higher than expected for a pathogenic variant in HBB causing Beta Thalassemia (1.2e-05 vs 1.10e-02), allowing no conclusion about variant significance. The variant, c.82G>T, has been reported in the literature in multiple individuals affected with Beta Thalassemia (Orkin_1984, Baklouti_1986, El-Kalla_1997, Tadmouri_1998, Sirdah_2013, Nasouhipur_2014). Clinical presentation ranged from mild to severe b-thal intermedia with a varying need for transfusions depending on the second pathogenic allele found. Based on the published reports, most cases have been diagnosed relatively late in childhood or puberty and some are much later in adulthood. Oxygen affinity studies showed a significantly decreased affinity for p.A28S for both heterozygous carriers and Hb Knossos-b-thalassemia compound heterozygotes (Fessas_1986). Two clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation and classified the variant as pathogenic/likely pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic. -
Pathogenic, no assertion criteria provided	clinical testing	Natera, Inc.	Sep 16, 2020	- -

Beta-Knossos-thalassemia

Pathogenic:1

Pathogenic, no assertion criteria provided

literature only

OMIM

Jan 01, 1989

- -

Malaria, susceptibility to

Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center

Apr 04, 2024

- -

Hb SS disease

Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Baylor Genetics

- -

Beta-plus-thalassemia

Pathogenic:1

Pathogenic, no assertion criteria provided

literature only

OMIM

Jan 01, 1989

- -

HEMOGLOBIN KNOSSOS

Other:1

other, no assertion criteria provided

literature only

OMIM

Dec 12, 2017

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.17

BayesDel_addAF

Pathogenic

0.21

BayesDel_noAF

Pathogenic

0.24

Cadd

Uncertain

Dann

Uncertain

1.0

DEOGEN2

Benign

0.062

T;T;.;T

Eigen

Benign

0.014

Eigen_PC

Benign

0.023

FATHMM_MKL

Uncertain

0.86

M_CAP

Benign

0.082

MetaRNN

Uncertain

0.60

D;D;D;D

MetaSVM

Uncertain

0.20

MutationAssessor

Uncertain

2.4

M;M;.;.

MutationTaster

Benign

1.0

PrimateAI

Uncertain

0.53

PROVEAN

Benign

-1.3

N;.;.;N

REVEL

Uncertain

0.64

Sift

Benign

0.030

D;.;.;D

Sift4G

Uncertain

0.057

T;.;.;.

Polyphen

0.27

B;B;.;.

Vest4

0.83

MVP

0.83

MPC

0.044

ClinPred

0.21

GERP RS

1.2

Varity_R

0.37

gMVP

0.82

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.79

Details are displayed if max score is > 0.2

DS_DG_spliceai

0.79

Position offset: 6

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over