11-5226597-C-T

Variant summary

Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PM1 PM2 PM5 PP3_Strong PP5_Very_Strong

The NM_000518.5(HBB):c.295G>A(p.Val99Met) variant causes a missense change. The variant allele was found at a frequency of 0.00000137 in 1,461,862 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 (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V99A) has been classified as Uncertain significance.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0000014 (0 hom.)
• Consequence: HBB NM_000518.5 missense
• Clinical Significance: Pathogenic criteria provided, multiple submitters, no conflicts P:6
• Conservation: PhyloP100: 7.20

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 18 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 chr11-5226596-A-T is described in Lovd as [Pathogenic].
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.983
• PP5: Variant 11-5226597-C-T is Pathogenic according to our data. Variant chr11-5226597-C-T is described in ClinVar as [Pathogenic]. Clinvar id is 15241.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-5226597-C-T is described in Lovd as [Pathogenic]. Variant chr11-5226597-C-T is described in Lovd as [Likely_pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HBB	NM_000518.5	c.295G>A	p.Val99Met	missense_variant	2/3	ENST00000335295.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HBB	ENST00000335295.4	c.295G>A	p.Val99Met	missense_variant	2/3	1	NM_000518.5	P1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD3 exomes AF: 0.00000398 AC: 1 AN: 251394 Hom.: 0 AF XY: 0.00000736 AC XY: 1 AN XY: 135852

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: 0.00

Gnomad NFE exome AF: 0.00000880

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.00000137 AC: 2 AN: 1461862 Hom.: 0 Cov.: 36 AF XY: 0.00000138 AC XY: 1 AN XY: 727234

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: 0.00000180

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:6

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Hemoglobinopathy Pathogenic:2

Pathogenic, no assertion criteria provided	literature only	OMIM	Dec 12, 2017	- -
Pathogenic, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Oct 04, 2019	Variant summary: HBB c.295G>A (p.Val99Met; also known as Hb Koln) 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 allele was found at a frequency of 4e-06 in 251394 control chromosomes (gnomAD). c.295G>A has been reported in the literature in heterozygous and compound heterozygous individuals presenting with clinical symptoms of Hemoglobinopathy and was observed to co-segregate with disease in an autosomal dominant manner (Chan_2010, Galacteros_1989, Huang_2011, Miller_1971). The occurrence of unstable hemoglobin and the presence of increased levels of reticulocytosis and Heinz bodies in those carrying the variant was described by a few of these studies. Several reports described the variant as the most common unstable hemoglobin (e.g. Coleman_1995). These data indicate that the variant is very likely to be associated with disease. A ClinVar submitter (evaluation after 2014) cites the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic. -

not provided Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital	Aug 15, 2023	- -
Pathogenic, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	Oct 17, 2023	The Hb Koln variant (HBB: c.295G>A; p.Val99Met, also known as Val98Met when numbered from the mature protein, rs33933298, HbVar ID: 448) is reported in the literature in multiple families diagnosed with mild hemolytic anemia, including several de novo cases, and is associated with Heinz body formation and splenomegaly (Hutchinson 1964, Jackson 1967, Jones, 1967, Landin 1994, Miller 1971, Stamatoyannopoulos 1981, HbVar database and references therein). Clinical symptoms are present in heterozygous individuals, and the variant co-segregates with disease in an autosomal dominant manner (Hutchinson 1964, Jackson 1967). In addition, this variant has been found in an individual with a beta(0) thalassemia variant who was reported to have almost pure Hb Koln in red blood cells and hemolytic anemia, but did not require blood transfusions or splenectomy (Galacteros 1989). This variant is listed in ClinVar (Variation ID: 15241), and is only observed on one allele in the Genome Aggregation Database, indicating it is not a common polymorphism. Functional analyses of the variant protein show decreased stability and an increase in the formation of inclusion bodies in red blood cells (Jones 1967, Miller 1971). Based on available information, this variant is considered to be pathogenic. References: HbVar link for HbVar: https://globin.bx.psu.edu/hbvar/hbvar.html Galacteros F et al. Hemoglobin Köln occurring in association with a beta zero thalassemia: hematologic and functional consequences. Blood. 1989 Jul;74(1):496-500. Hutchinson HE et al. Hereditary Heinz-body anaemia, thrombocytopenia, and haemogloblinopathy (Hb Koeln) in a Glasgow family. Br Med J. 1964 Oct 31;2(5417):1099-103. Jackson JM et al. A West Australian family with a haemolytic disorder associated with haemoglobin Koln. Br J Haematol. 1967 Jul;13(4):474-81. Jones RV et al. Koln haemoglobinopathy. Further data and a comparison with other hereditary Heinz body anaemias. Br J Haematol. 1967 May;13(3):394-408. Landin B et al. Haemoglobin Köln as de novo mutations in Sweden: diagnosis by PCR and specific enzymatic cleavage. Eur J Haematol. 1994 Mar;52(3):156-61. Miller DR et al. Hemoglobin Koln disease occurring as a fresh mutation: erythrocyte metabolism and survival. Blood. 1971 Dec;38(6):715-29. -

beta Thalassemia Pathogenic:1

Pathogenic, no assertion criteria provided

clinical testing

Natera, Inc.

Mar 17, 2017

- -

Heinz body anemia Pathogenic:1

Pathogenic, no assertion criteria provided

literature only

OMIM

Mar 01, 1995

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.98
BayesDel_addAF	Pathogenic	0.54	D
BayesDel_noAF	Pathogenic	0.54
Cadd	Uncertain	25
Dann	Uncertain	1.0
DEOGEN2	Benign	0.20	T;T;.
Eigen	Pathogenic	0.91
Eigen_PC	Pathogenic	0.83
FATHMM_MKL	Pathogenic	0.97	D
M_CAP	Pathogenic	0.45	D
MetaRNN	Pathogenic	0.98	D;D;D
MetaSVM	Pathogenic	1.1	D
MutationAssessor	Pathogenic	3.9	H;H;.
MutationTaster	Benign	1.0	D
PrimateAI	Uncertain	0.76	T
PROVEAN	Uncertain	-2.6	D;.;.
REVEL	Pathogenic	0.90
Sift	Pathogenic	0.0	D;.;.
Sift4G	Pathogenic	0.0	D;.;.
Polyphen		1.0	D;D;.
Vest4		0.97
MutPred		0.94		Gain of ubiquitination at K96 (P = 0.1062);Gain of ubiquitination at K96 (P = 0.1062);Gain of ubiquitination at K96 (P = 0.1062);
MVP		0.95
MPC		0.25
ClinPred		0.99	D
GERP RS		5.2
Varity_R		0.80
gMVP		0.96

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: rs33933298; hg19: chr11-5247827;