11-5227018-C-T

Variant names:

• chr11-5227018-C-T
• rs33958358
• NM_000518.5:c.4G>A

Variant summary

Our verdict is Uncertain significance. Variant got 5 ACMG points: 6P and 1B. PM2 PM5 PP3_Moderate BP6

The NM_000518.5(HBB):​c.4G>A​(p.Val2Met) variant causes a missense change. The variant allele was found at a frequency of 0.00000624 in 1,443,092 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 Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V2A) has been classified as Pathogenic.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0000062 (0 hom.)
• Consequence: HBB NM_000518.5 missense
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:3 B:2 O:1
• Conservation: PhyloP100: 3.94

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 Uncertain_significance. Variant got 5 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PM5: Other missense variant is known to change same aminoacid residue: Variant chr11-5227017-A-G is described in Lovd as [Pathogenic].
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.894
• BP6: Variant 11-5227018-C-T is Benign according to our data. Variant chr11-5227018-C-T is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 15359.We mark this variant Likely_benign, oryginal submissions are: {Likely_benign=1, Uncertain_significance=2}.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HBB	NM_000518.5	c.4G>A	p.Val2Met	missense_variant	Exon 1 of 3	ENST00000335295.4	NP_000509.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HBB	ENST00000335295.4	c.4G>A	p.Val2Met	missense_variant	Exon 1 of 3	1	NM_000518.5	ENSP00000333994.3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD3 exomes AF: 0.00000398 AC: 1 AN: 251128 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 135724

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: 0.00000881

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.00000624 AC: 9 AN: 1443092 Hom.: 0 Cov.: 26 AF XY: 0.00000278 AC XY: 2 AN XY: 719252

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: 0.00000822

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

EpiCase AF: 0.00

EpiControl AF: 0.0000593

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Uncertain:3 Benign:2 Other:1

Revision: criteria provided, conflicting classifications

Submissions by phenotype

not specified Uncertain:2

Mar 21, 2017

Quest Diagnostics Nichols Institute San Juan Capistrano

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Apr 19, 2019

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

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant summary: HBB c.4G>A (p.Val2Met; also known as Hb South Florida) results in a conservative amino acid change in the encoded protein sequence. Three 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 251128 control chromosomes (gnomAD). The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. The variant is known to interfere with some methods of HbA1c determination and has been (falsely) reported in several carriers as elevated HbA1c, but without clinical evidence of any hematologic abnormality (Shah 1986, Aslanger 2013, Celebiler 2014, Canatan 2016). These data indicate that this variant does not produce any clinical symptoms in heterozygous state. According to our knowledge, only one compound heterozygous individual has been reported in the literature who carried a pathogenic variant (c.92+1G>A) for beta-0-thalassemia in trans, and presented with beta-thalassemia trait without clinical manifestations (Tan 2006, Tan 2009). Since compound heterozygosity for two pathogenic variants would result in a more severe phenotype, this report provides supportive evidence for a benign role (Tan 2009). Early reports demonstrated that the variant prevents the cleavage of the initiator methionine (Boissel 1985), but does not result in an unstable hemoglobin (Shah 1986). However, to our knowledge no other studies performed further functional characterization, thus allowing no convincing conclusions about the variant effect. One clinical diagnostic laboratory has submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation, and classified the variant as uncertain significance. Based on the evidence outlined above, the variant was classified as VUS-possibly benign. -

beta Thalassemia Uncertain:1 Benign:1

Aug 19, 2020

Natera, Inc.

Significance: Uncertain significance

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Sep 08, 2023

Molecular Genetics Laboratory, BC Children's and BC Women's Hospitals

Significance: Likely benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

not provided Benign:1

Feb 01, 2024

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The Hb South Florida variant (HBB: c.4G>A; p.Val2Met, also known as Val1Met when numbered from the mature protein, rs33958358, HbVar ID: 713) is reported in the heterozygous state in asymptomatic individuals (Shah 1986). Additionally, it has been reported compound heterozygous with a pathogenic HBB variant in an individual presenting only with beta-thalassemia trait, suggesting a neutral effect for the Hb South Florida variant (Tan 2006 and 2009). Functional studies report this variant interferes with measurements of HbA1c (Boissel 1985, Shah 1986). This variant is reported in ClinVar (Variation ID: 15359). It is only found on one allele in the Genome Aggregation Database, indicating it is not a common polymorphism. Computational analyses predict that this variant is deleterious (REVEL: 0.82). Based on available information this variant is considered to be likely benign. References: Link to HbVar database: https://globin.bx.psu.edu/hbvar/menu.html Boissel JP et al. Amino-terminal processing of proteins: hemoglobin South Florida, a variant with retention of initiator methionine and N alpha-acetylation. Proc Natl Acad Sci U S A. 1985 Dec;82(24):8448-52. PMID: 3866233. Shah SC et al. Hemoglobin South Florida. New variant with normal electrophoretic pattern mistaken for glycosylated hemoglobin. Diabetes. 1986 Oct;35(10):1073-6. PMID: 3758492. Tan JA et al. Characterisation and confirmation of rare beta-thalassaemia mutations in the Malay, Chinese and Indian ethnic groups in Malaysia. Pathology. 2006 Oct;38(5):437-41. PMID: 17008283. Tan JA et al. Interaction of Hb South Florida (codon 1; GTG-->ATG) and HbE, with beta-thalassemia (IVS1-1; G-->A): expression of different clinical phenotypes. Eur J Pediatr. 2009 Sep;168(9):1049-54. PMID: 19034506. -

HEMOGLOBIN SOUTH FLORIDA 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	0.89
BayesDel_addAF	Pathogenic	0.34	D
BayesDel_noAF	Pathogenic	0.25
CADD	Benign	23
DANN	Uncertain	0.99
DEOGEN2	Benign	0.028	T;T;.;T
Eigen	Uncertain	0.31
Eigen_PC	Uncertain	0.25
FATHMM_MKL	Uncertain	0.97	D
LIST_S2	Uncertain	0.91	.;D;D;D
M_CAP	Pathogenic	0.51	D
MetaRNN	Pathogenic	0.89	D;D;D;D
MetaSVM	Uncertain	0.59	D
MutationAssessor	Benign	1.5	L;L;.;.
PrimateAI	Uncertain	0.74	T
PROVEAN	Benign	-2.0	N;.;.;N
REVEL	Pathogenic	0.82
Sift	Benign	0.089	T;.;.;T
Sift4G	Benign	0.12	T;.;.;.
Polyphen		1.0	D;D;.;.
Vest4		0.88
MutPred		0.71		Gain of glycosylation at P6 (P = 0.0852);Gain of glycosylation at P6 (P = 0.0852);Gain of glycosylation at P6 (P = 0.0852);Gain of glycosylation at P6 (P = 0.0852);
MVP		0.76
MPC		0.14
ClinPred		0.88	D
GERP RS		4.2
Varity_R		0.21
gMVP		0.78

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: rs33958358; hg19: chr11-5248248;