rs1135071

chr11-5226799-C-Achr11-5226799-C-Gchr11-5226799-C-T

Variant summary

Our verdict is Likely pathogenic. Variant got 7 ACMG points: 7P and 0B. PM1 PM2 PM5 PP3

The NM_000518.5(HBB):c.93G>T(p.Arg31Ser) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000138 in 1,613,862 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 2/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Uncertain significance (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Pathogenicin ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R31G) has been classified as Pathogenic.

• Frequency:
  • Genomes: 𝑓 0.00025 (0 hom., cov: 32)
  • Exomes 𝑓: 0.00013 (0 hom.)
• Consequence: HBB NM_000518.5 missense, splice_region
• Scores: Splicing: ADA: 0.9987
• Clinical Significance: Uncertain significance criteria provided, multiple submitters, no conflicts P:2 U:6
• Conservation: PhyloP100: 1.84

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 7 ACMG points.

• PM1: In a hotspot region, there are 9 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 1 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 chr11-5226930-C-T is described in ClinVar as [Likely_pathogenic]. Clinvar id is 36337.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• PP3: Splicing scoreres supports a deletorius effect: Scorers claiming Pathogenic: dbscSNV1_ADA, dbscSNV1_RF. No scorers claiming Uncertain. Scorers claiming Benign: max_spliceai.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HBB	NM_000518.5	c.93G>T	p.Arg31Ser	missense_variant, splice_region_variant	2/3	ENST00000335295.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HBB	ENST00000335295.4	c.93G>T	p.Arg31Ser	missense_variant, splice_region_variant	2/3	1	NM_000518.5	P1

Frequencies

GnomAD3 genomes AF: 0.000250 AC: 38 AN: 152152 Hom.: 0 Cov.: 32

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: 0.00339

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000294

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.000346 AC: 87 AN: 251316 Hom.: 0 AF XY: 0.000280 AC XY: 38 AN XY: 135804

Gnomad AFR exome AF: 0.00

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: 0.00365

Gnomad NFE exome AF: 0.0000440

Gnomad OTH exome AF: 0.000489

GnomAD4 exome AF: 0.000126 AC: 184 AN: 1461592 Hom.: 0 Cov.: 36 AF XY: 0.000107 AC XY: 78 AN XY: 727138

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: 0.00328

Gnomad4 NFE exome AF: 0.00000180

Gnomad4 OTH exome AF: 0.000116

GnomAD4 genome AF: 0.000250 AC: 38 AN: 152270 Hom.: 0 Cov.: 32 AF XY: 0.000389 AC XY: 29 AN XY: 74464

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: 0.00339

Gnomad4 NFE AF: 0.0000294

Gnomad4 OTH AF: 0.00

Alfa AF: 0.0000407 Hom.: 0

Bravo AF: 0.00000378

ExAC AF: 0.000280 AC: 34

ClinVar

Significance: Uncertain significance

Submissions summary: Pathogenic:2 Uncertain:6

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Uncertain:3

Uncertain significance, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	Mar 02, 2022	The Hb Tacoma variant (HBB: c.93G>T; p.Arg31Ser, also known as Arg30Ser when numbered from the mature protein, HbVar ID: 289, rs1135071) is reported in the literature in the heterozygous state in individuals with mild anemia or no symptoms (Deacon-Smith 1978, Idelson 1974, Landin 1993), and in one individual with Hb S who had sickle cell trait (Honig 1980). This variant is also reported in ClinVar (Variation ID: 15368) and is found in the Finnish European population with an allele frequency of 0.36% (90/25120 alleles) in the Genome Aggregation Database. The arginine at codon 31 is highly conserved, and computational analyses predict that this variant is deleterious (REVEL: 0.947). This variant is the first nucleotide of the exon, and computational analyses (Alamut v.2.11) predict that this variant may impact splicing by weakening the nearby canonical acceptor splice site. Functional analyses demonstrate a normal oxygen affinity but slight instability (Deacon-Smith 1978, Honig 1980). Due to conflicting information, the clinical significance of the Hb Tacoma variant is uncertain at this time. References: Link to HbVar database: https://globin.bx.psu.edu/hbvar/menu.html Deacon-Smith RA and Lee-Potter JP. An unstable haemoglobin, Hb Tacoma beta30 (B12) arg leads to ser, detected at birth by the demonstration of red cell inclusions. J Clin Pathol. 1978 Sep;31(9):883-7. PMID: 711920. Honig GR et al. Two new sickle cell syndromes: HbS, Hb Camden, and alpha-thalassemia; and HbS in combination with Hb Tacoma. Blood. 1980 Apr;55(4):655-60. PMID: 7357091. Idelson LI et al. New unstable haemoglobin (Hb Moscva, beta24 (B4) Gly leads to Asp) found in the USSR. Nature. 1974 Jun 21;249(459):768-70. PMID: 4525423. Landin B and Jeppsson JO. Rare beta chain hemoglobin variants found in Swedish patients during HBA1c analysis. Hemoglobin. 1993 Aug;17(4):303-18. PMID: 8226093. -
Uncertain significance, criteria provided, single submitter	clinical testing	Quest Diagnostics Nichols Institute San Juan Capistrano	Jun 18, 2023	The HBB c.93G>T (p.Arg31Ser) variant (also known as Hb Tacoma) has been reported to have normal oxygen affinity but slightly reduced stability (PMIDs: 31553106 (2020), 7357091 (1980), 5785231 (1969), 5869485 (1965)). Individuals who are heterozygous for this variant have normal presentations (PMID: 5869485 (1965)) or mild anemia (PMIDs: 34233561 (2021), 8226093 (1993), 3937827 (1985)). Co-occurrence of this variant with Hb S presented as clinically healthy (PMID: 7357091 (1980)), but in combination with a beta(+)-thalassemia variant resulted in moderate microcytic anemia (PMID: 10975446 (2000)). Additionally, an individual who was compound heterozygous for Hb Tacoma caused by a different nucleotide change (c.93G>C, p.Arg31Ser) and a HBB pathogenic variant associated with beta(0)-thalassemia is reported to have transfusion-dependent beta thalassemia (PMID: 9140720 (1997)). Analysis of this variant using bioinformatics tools indicates that the effect of this variant's amino acid change on protein structure and function is damaging, and it may also affect proper HBB mRNA splicing. Clinical correlation and genetic counseling are recommended. -
Uncertain significance, criteria provided, single submitter	clinical testing	Invitae	Jun 21, 2018	This sequence change replaces arginine with serine at codon 31 of the HBB protein (p.Arg31Ser). The arginine residue is highly conserved and there is a moderate physicochemical difference between arginine and serine. This variant is present in population databases (rs1135071, ExAC 0.3%). This variant has been observed in individuals and families with elevated Hb A2 levels, but most individuals are either clinically unaffected or experience only mild anemia (PMID: 8226093, 4525423, 5869485, 3937827, 7357091). This variant is also known as Arg30Ser and Hb Tacoma in the literature. ClinVar contains an entry for this variant (Variation ID: 15368). Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Tolerated"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0". The serine amino acid residue is found in multiple mammalian species, suggesting that this missense change does not adversely affect protein function. These predictions have not been confirmed by published functional studies and their clinical significance is uncertain. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site, but this prediction has not been confirmed by published transcriptional studies. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -

not specified Pathogenic:1 Uncertain:1

Pathogenic, flagged submission	literature only	OMIM	Feb 01, 2002	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Nov 11, 2019	Variant summary: HBB c.93G>T (p.Arg31Ser, also known as Hb Tacoma) results in a non-conservative amino acid change located in the Globin domain (IPR000971) of the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. 5/5 computational tools predict no significant impact on normal splicing. However, these predictions have yet to be confirmed by functional studies. The variant allele was found at a frequency of 0.00035 in 251316 control chromosomes (gnomAD). This frequency is not significantly higher than expected for a pathogenic variant in HBB causing Beta Thalassemia (0.00035 vs 0.011), allowing no conclusion about variant significance. Hb Tacoma is used to describe the substitution of Arg-to-Ser at codon 31 (legacy codon 30) and can be due to either c.93G>T or c.93G>C. It has been reported in the literature in heterozygous individuals with no clinical or hematological abnormalities apart from mild anemia (Deacon-Smith_1978, Harano_1985) and in one heterozygous individual who also carried Hb S and had normal hematological findings (Honig_1980). c.93G>T in particular was reported in heterozygous individuals with normal hematological findings in some of them and slight hemolytic anemia in others, while importantly it was also reported in a 12-year-old boy in compound heterozygosity with pathogenic variant c.93-21G>A and no signs of disease (Landin 1993, 2000). These reports do not provide unequivocal conclusions about association of the variant with Beta Thalassemia. Experimental evidence evaluating an impact on protein function demonstrate the variant to display in vitro instability, including a decreased alkaline Bohr effect and haem--haem interaction but normal oxygen affinity (Deacon-Smith_1978, Hayashi_1974). These data do not allow convincing conclusions about the variant effect. 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 uncertain significance. -

Heinz body anemia Pathogenic:1

Pathogenic, no assertion criteria provided

literature only

OMIM

Feb 01, 2002

- -

beta Thalassemia Uncertain:1

Uncertain significance, no assertion criteria provided

clinical testing

Natera, Inc.

Mar 16, 2021

- -

Beta-thalassemia HBB/LCRB Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

MGZ Medical Genetics Center

Nov 26, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.95
BayesDel_addAF	Pathogenic	0.38	D
BayesDel_noAF	Pathogenic	0.46
Cadd	Uncertain	25
Dann	Uncertain	1.0
DEOGEN2	Benign	0.16	T;T;.;T
Eigen	Uncertain	0.59
Eigen_PC	Uncertain	0.46
FATHMM_MKL	Uncertain	0.85	D
M_CAP	Pathogenic	0.74	D
MetaRNN	Benign	0.084	T;T;T;T
MetaSVM	Pathogenic	1.1	D
MutationAssessor	Pathogenic	3.4	M;M;.;.
MutationTaster	Benign	1.0	D
PrimateAI	Uncertain	0.67	T
PROVEAN	Uncertain	-4.2	D;.;.;D
REVEL	Pathogenic	0.95
Sift	Uncertain	0.020	D;.;.;D
Sift4G	Uncertain	0.029	D;.;.;.
Polyphen		1.0	D;D;.;.
Vest4		0.63
MutPred		0.87		Gain of loop (P = 0.1069);Gain of loop (P = 0.1069);Gain of loop (P = 0.1069);Gain of loop (P = 0.1069);
MVP		0.99
MPC		0.26
ClinPred		0.33	T
GERP RS		4.2
Varity_R		0.89
gMVP		0.95

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	1.0
dbscSNV1_RF	Pathogenic	0.97
SpliceAI score (max)		0.020		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: rs1135071; hg19: chr11-5248029;