11-5226690-C-T

Variant names:

• chr11-5226690-C-T
• rs36008922
• NM_000518.5:c.202G>A

Variant summary

Our verdict is Pathogenic. Variant got 16 ACMG points: 16P and 0B. PM2 PM5 PP3_Strong PP5_Very_Strong

The NM_000518.5(HBB):​c.202G>A​(p.Val68Met) variant causes a missense change. 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 Pathogenic (★★). Another nucleotide change resulting in the same amino acid substitution has been previously reported as Likely benign in UniProt. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V68A) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 32)
• Consequence: HBB NM_000518.5 missense
• Clinical Significance: Pathogenic criteria provided, multiple submitters, no conflicts P:2 O:2
• Conservation: PhyloP100: 3.64

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 Pathogenic. Variant got 16 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PM5: Other missense variant is known to change same aminoacid residue: Variant chr11-5226689-A-C is described in Lovd as [Pathogenic].
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.983
• PP5: Variant 11-5226690-C-T is Pathogenic according to our data. Variant chr11-5226690-C-T is described in ClinVar as [Pathogenic]. Clinvar id is 15536.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-5226690-C-T is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HBB	NM_000518.5	c.202G>A	p.Val68Met	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.202G>A	p.Val68Met	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: Pathogenic

Submissions summary: Pathogenic:2 Other:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Hemoglobinopathy Pathogenic:1

Nov 06, 2024

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.202G>A (p.Val68Met) results in a conservative amino acid change located in the Globin domain 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 251432 control chromosomes. c.202G>A has been reported in the literature in heterozygous state in multiple individuals affected with severe Haemolytic anaemia and were transfusion dependent in the early years of life (examples: Molchanova_1993, Jiang_2016, Pedroso_2017, Hamid_2019, Su_2019, Corrons_2022, Zhang_2023). These data indicate that the variant is very likely to be associated with disease. At-least two of these cases were reported as de novo (Pedroso_ 2017, Hamid_ 2019) however, most published cases were without a family history for the disease (Table 1 in Zhang_2023). The following publications have been ascertained in the context of this evaluation (PMID: 8330974, 28361590, 28670945, 30316205, 31084366, 35091138, 37457725). ClinVar contains an entry for this variant (Variation ID: 15536). Based on the evidence outlined above, the variant was classified as pathogenic. -

not provided Pathogenic:1

Nov 05, 2024

Quest Diagnostics Nichols Institute San Juan Capistrano

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The HBB c.202G>A (p.Val68Met) variant (also known as Hb Bristol, Hb Alesha, Hb Bristol-Alesha) has been characterized as a unstable hemoglobin variant, reported in the heterozygous state in multiple individuals with transfusion-dependent, severe hemolytic anemia (PMIDs: 37457725 (2023), 35091138 (2022), 17654076 (2007), 15646651 (2004), 8704193 (1996), 8330974 (1993)), and occurred as a de novo variant in two families (PMIDs: 28670945 (2017), 30316205 (2019)). This variant has not been reported in large, multi-ethnic general populations (Genome Aggregation Database, http://gnomad.broadinstitute.org). Analysis of this variant using bioinformatics tools for the prediction of the effect of amino acid changes on protein structure and function yielded predictions that this variant is damaging. Based on the available information, this variant is classified as pathogenic. -

HEMOGLOBIN ALESHA Other:1

Jun 01, 1993

OMIM

Significance: other

Review Status: no assertion criteria provided

Collection Method: literature only

- -

HEMOGLOBIN BRISTOL Other:1

Dec 12, 2017

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	0.98
BayesDel_addAF	Pathogenic	0.51	D
BayesDel_noAF	Pathogenic	0.49
CADD	Uncertain	25
DANN	Uncertain	1.0
DEOGEN2	Benign	0.21	T;T;.;T
Eigen	Pathogenic	0.76
Eigen_PC	Pathogenic	0.68
FATHMM_MKL	Uncertain	0.93	D
LIST_S2	Uncertain	0.94	.;D;D;D
M_CAP	Pathogenic	0.41	D
MetaRNN	Pathogenic	0.98	D;D;D;D
MetaSVM	Pathogenic	1.1	D
MutationAssessor	Pathogenic	3.4	M;M;.;.
PrimateAI	Uncertain	0.69	T
PROVEAN	Uncertain	-2.5	D;.;.;D
REVEL	Pathogenic	0.89
Sift	Pathogenic	0.0	D;.;.;D
Sift4G	Uncertain	0.024	D;.;.;.
Polyphen		1.0	D;D;.;.
Vest4		0.70
MutPred		0.94		Gain of disorder (P = 0.0695);Gain of disorder (P = 0.0695);Gain of disorder (P = 0.0695);Gain of disorder (P = 0.0695);
MVP		0.85
MPC		0.17
ClinPred		0.98	D
GERP RS		5.1
Varity_R		0.67
gMVP		0.89

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: rs36008922; hg19: chr11-5247920;