11-5226774-G-T

Variant summary

Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PM1 PM2 PP3

The NM_000518.5(HBB):c.118C>A(p.Gln40Lys) 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 Uncertain significance (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. Q40E) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: HBB NM_000518.5 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1 O:1
• 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 Uncertain_significance. Variant got 5 ACMG points.

• PM1: In a hotspot region, there are 6 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 4 benign, 16 uncertain in NM_000518.5
• PM2: Very rare variant in population databases, with high coverage
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.819

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HBB	NM_000518.5	c.118C>A	p.Gln40Lys	missense_variant	2/3	ENST00000335295.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HBB	ENST00000335295.4	c.118C>A	p.Gln40Lys	missense_variant	2/3	1	NM_000518.5	P1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 36

GnomAD4 genome Cov.: 32

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1 Other:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

Nov 25, 2020

The Hb Alabama variant (HBB: c.118C>A; p.Gln40Lys, also known as Gln39Lys when numbered from the mature protein, rs11549407), is reported in the literature in the heterozygous state in at least one individual affected with mild anemia (see link to HbVar and references therein). This variant is also reported in ClinVar (Variation ID: 811501), but is absent from general population databases (Exome Variant Server, and Genome Aggregation Database), indicating it is not a common polymorphism. Additionally, other amino acid substitutions at this codon (Glu, Pro, Arg) have been reported in heterozygous individuals with symptoms ranging from hemolytic mild anemia to no clinical symptoms (Hb Vaasa, Hb Hyden, Hb Tianshui in HbVar and references therein). The glutamine at codon 40 is highly conserved, and computational analyses predict that this variant is deleterious (REVEL: 0.733). Due to limited information, the clinical significance of the Hb Alabama variant is uncertain at this time. References: Link to HbVar for Hb Alabama: http://globin.bx.psu.edu/cgi-bin/hbvar/query_vars3?mode=output&display_format=page&i=307 -

HEMOGLOBIN ALABAMA Other:1

other, no assertion criteria provided

literature only

OMIM

Dec 12, 2017

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.41
BayesDel_addAF	Pathogenic	0.26	D
BayesDel_noAF	Uncertain	0.13
Cadd	Uncertain	24
Dann	Uncertain	1.0
DEOGEN2	Benign	0.069	T;T;.;T
Eigen	Uncertain	0.41
Eigen_PC	Uncertain	0.45
FATHMM_MKL	Uncertain	0.87	D
M_CAP	Uncertain	0.15	D
MetaRNN	Pathogenic	0.82	D;D;D;D
MetaSVM	Uncertain	0.56	D
MutationAssessor	Benign	1.3	L;L;.;.
MutationTaster	Benign	1.0	D
PrimateAI	Uncertain	0.58	T
PROVEAN	Uncertain	-3.4	D;.;.;D
REVEL	Pathogenic	0.73
Sift	Uncertain	0.0020	D;.;.;D
Sift4G	Benign	0.40	T;.;.;.
Polyphen		0.83	P;P;.;.
Vest4		0.59
MutPred		0.64		Gain of methylation at Q40 (P = 8e-04);Gain of methylation at Q40 (P = 8e-04);Gain of methylation at Q40 (P = 8e-04);Gain of methylation at Q40 (P = 8e-04);
MVP		0.93
MPC		0.075
ClinPred		0.94	D
GERP RS		4.1
Varity_R		0.81
gMVP		0.72

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: rs11549407; hg19: chr11-5248004;