rs33922873

Variant names:

• chr11-5226702-G-A
• rs33922873
• NM_000518.5:c.190C>T

Your query was ambiguous. Multiple possible variants found:

• chr11-5226702-G-A
• chr11-5226702-G-T

Variant summary

Our verdict is Likely pathogenic. Variant got 9 ACMG points: 9P and 0B. PM2 PM5 PP3_Strong PP5

The NM_000518.5(HBB):​c.190C>T​(p.His64Tyr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. H64R) has been classified as Pathogenic.

• Frequency: Genomes: not found (cov: 32)
• Consequence: HBB NM_000518.5 missense
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:5 U:1 O:1
• Conservation: PhyloP100: 9.10

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]

ACMG classification

Verdict is Likely_pathogenic. Variant got 9 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PM5: Other missense variant is known to change same aminoacid residue: Variant chr11-5226701-T-C is described in Lovd as [Pathogenic].
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.989
• PP5: Variant 11-5226702-G-A is Pathogenic according to our data. Variant chr11-5226702-G-A is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 15256.We mark this variant Likely_pathogenic, oryginal submissions are: {Uncertain_significance=1, Pathogenic=4}. Variant chr11-5226702-G-A is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HBB	NM_000518.5	c.190C>T	p.His64Tyr	missense_variant	Exon 2 of 3	ENST00000335295.4	NP_000509.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HBB	ENST00000335295.4	c.190C>T	p.His64Tyr	missense_variant	Exon 2 of 3	1	NM_000518.5	ENSP00000333994.3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 36

GnomAD4 genome Cov.: 32

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:5 Uncertain:1 Other:1

Revision: criteria provided, conflicting classifications

Submissions by phenotype

beta Thalassemia Pathogenic:2

May 28, 2019

Mendelics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Jul 02, 2019

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant summary: HBB c.190C>T (p.His64Tyr) results in a conservative amino acid change located in a heme binding site (InterPro) of the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. The variant was absent in 251426 control chromosomes (gnomAD). The variant (also known as Hb M-Saskatoon) is widely regarded as causing hemoglobin M (HbM) disease, and has been reported in the literature in several affected individuals (e.g. Efremov_1974, Waye_1994, Suryantoro_1995, Kedar_2005, Brunner-Agten_2010, Garcia-Morin_2019). The disorder was observed to be inherited in an autosomal dominant pattern, often occurring as a de novo mutation. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. 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. -

not provided Pathogenic:1 Uncertain:1

Mar 05, 2024

Quest Diagnostics Nichols Institute San Juan Capistrano

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The HBB c.190C>T (p.His64Tyr) variant (also known as Hb M Saskatoon and H63Y) has been reported in the published literature in individuals/families affected with autosomal dominant methemoglobinemia (PMIDs: 34789072 (2021), 4841979 (1974), 13897827 (1961), 20324533 (1950)) and has been observed to occur de novo (PMIDs: 19727720 (2010), 15929117 (2005), 7713749 (1994)). Functional studies have reported that this variant shows increased oxygen affinity, increased auto-oxidation, and reduced stability (PMIDs: 15929117 (2005), 4086306 (1985), 7372598 (1980), 6248489 (1980), 4301455 (1968), 5851873 (1965)). This variant has not been reported in large, multi-ethnic general populations (Genome Aggregation Database, http://gnomad.broadinstitute.org). Based on the available information, this variant is associated with autosomal dominant methemoglobinemia, however, we are unable to determine the clinical significance of this variant as it relates to the severity of beta thalassemia when a pathogenic variant occurs in trans. Testing affected family members could help clarify the clinical significance of this variant. Genetic counseling is recommended. -

Jan 22, 2024

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The Hb M-Saskatoon variant (HBB: c.190C>T; p.His64Tyr, also known as His63Tyr when numbered from the mature protein, rs33922873, HbVar ID: 359) is reported in the literature in several individuals with hemoglobin M (HbM) disease (Arbane-Dahmane 1985, Bouatrous 2021, Brunner-Agten 2010, Gottgens 2021, Suryantoro 1995, Waye 1994). HbM disease is an autosomal dominantly inherited congenital form of methemoglobinemia, and pathogenic variants often occur de novo (Bouatrous 2021, Brunner-Agten 2010, Waye 1994). This variant is reported in ClinVar (Variation ID: 15256). It is absent from the Genome Aggregation Database, indicating it is not a common polymorphism. Computational analyses predict that this variant is deleterious (REVEL: 0.942). Based on available information, the Hb M-Saskatoon variant is considered to be pathogenic for HbM disease. References: Link to HbVar database: https://globin.bx.psu.edu/hbvar/menu.html Arbane-Dahmane M et al. Hemoglobin M Saskatoon (alpha 2 beta 2 63(E7) His----Tyr) in an Algerian family. Hemoglobin. 1985;9(5):509-11. PMID: 4086306. Bouatrous E et al. First Observation of HbM-Saskatoon at the Origin of Neonatal Cyanosis in a Tunisian Baby. J Pediatr Hematol Oncol. 2021 Nov 1;43(8):e1055-e1058. PMID: 33625083. Brunner-Agten S et al. Compound heterozygosity of Hb Hamilton and de novo mutated HbM Saskatoon. Ann Hematol. 2010 May;89(5):517-8. PMID: 19727720. Gottgens EL et al. Cyanosis, hemolysis, decreased HbA1c and abnormal co-oximetry in a patient with hemoglobin M Saskatoon (HBB:c.190C?>?T p.His64Tyr). Hematology. 2021 Dec;26(1):914-918. PMID: 34789072. Suryantoro P et al. C to T transition at the first nucleotide of codon 63 of the beta-globin gene corresponding to hemoglobin M-Saskatoon in an Indonesian boy. Jpn J Hum Genet. 1995 Jun;40(2):195-201. PMID: 7663000. Waye JS et al. De novo beta-globin gene mutation (beta 63(E7)His-->Tyr) giving rise to Hb M disease in a Newfoundlander. Hemoglobin. 1994 Nov;18(6):441-3. PMID: 7713749. -

Inborn genetic diseases Pathogenic:1

Apr 16, 2019

Ambry Genetics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

HEMOGLOBIN M (RADOM) METHEMOGLOBINEMIA, BETA TYPE Pathogenic:1

Jun 01, 1995

OMIM

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: literature only

- -

HEMOGLOBIN M (SASKATOON) Other:1

May 10, 2018

OMIM

Significance: other

Review Status: no assertion criteria provided

Collection Method: literature only

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.97
BayesDel_addAF	Pathogenic	0.55	D
BayesDel_noAF	Pathogenic	0.55
CADD	Pathogenic	26
DANN	Uncertain	1.0
DEOGEN2	Benign	0.28	T;T;.;T
Eigen	Pathogenic	0.90
Eigen_PC	Pathogenic	0.84
FATHMM_MKL	Pathogenic	0.98	D
LIST_S2	Uncertain	0.90	.;D;D;D
M_CAP	Pathogenic	0.39	D
MetaRNN	Pathogenic	0.99	D;D;D;D
MetaSVM	Pathogenic	1.1	D
MutationAssessor	Pathogenic	4.3	H;H;.;.
PrimateAI	Uncertain	0.61	T
PROVEAN	Pathogenic	-5.7	D;.;.;D
REVEL	Pathogenic	0.94
Sift	Uncertain	0.0030	D;.;.;D
Sift4G	Uncertain	0.0050	D;.;.;.
Polyphen		0.96	D;D;.;.
Vest4		0.98
MutPred		0.95		Loss of disorder (P = 0.0359);Loss of disorder (P = 0.0359);Loss of disorder (P = 0.0359);Loss of disorder (P = 0.0359);
MVP		0.98
MPC		0.086
ClinPred		0.99	D
GERP RS		5.1
Varity_R		0.84
gMVP		0.99

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

Other links and lift over

dbSNP: rs33922873; hg19: chr11-5247932;