16-173229-T-C

Variant names:

• chr16-173229-T-C
• rs41323248
• NM_000517.6:c.200T>C

Variant summary

Our verdict is Pathogenic. The variant received 14 ACMG points: 14P and 0B. PM1 PP3_Strong PP5_Very_Strong

The NM_000517.6(HBA2):​c.200T>C​(p.Leu67Pro) variant causes a missense change involving the alteration of a conserved nucleotide. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. L67Q) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 20)
• Consequence: HBA2 NM_000517.6 missense
• Clinical Significance: Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:2 O:1
• Conservation: PhyloP100: 7.47
• Publications: 2 publications found

Genes affected

HBA2 (HGNC:4824): (hemoglobin subunit alpha 2) The human alpha globin gene cluster located on chromosome 16 spans about 30 kb and includes seven loci: 5'- zeta - pseudozeta - mu - pseudoalpha-1 - alpha-2 - alpha-1 - theta - 3'. The alpha-2 (HBA2) and alpha-1 (HBA1) coding sequences are identical. These genes differ slightly over the 5' untranslated regions and the introns, but they differ significantly over the 3' untranslated regions. Two alpha chains plus two beta chains constitute HbA, which in normal adult life comprises about 97% of the total hemoglobin; alpha chains combine with delta chains to constitute HbA-2, which with HbF (fetal hemoglobin) makes up the remaining 3% of adult hemoglobin. Alpha thalassemias result from deletions of each of the alpha genes as well as deletions of both HBA2 and HBA1; some nondeletion alpha thalassemias have also been reported. [provided by RefSeq, Jul 2008]

HBA2 Gene-Disease associations (from GenCC):

• alpha thalassemia spectrum

  Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), ClinGen
• erythrocytosis, familial, 7

  Inheritance: AD Classification: STRONG, LIMITED Submitted by: Genomics England PanelApp, Labcorp Genetics (formerly Invitae)
• hemoglobin M disease

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• Hb Bart's hydrops fetalis

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
• hemoglobin H disease

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
• Heinz body anemia

  Inheritance: AD Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae)
• methemoglobinemia, alpha type

  Inheritance: AD Classification: LIMITED Submitted by: ClinGen

ENSG00000294455 (HGNC:):

ACMG classification

Our verdict: Pathogenic. The variant received 14 ACMG points.

• PM1: In a hotspot region, there are 3 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 3 benign, 8 uncertain in NM_000517.6
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.995
• PP5: Variant 16-173229-T-C is Pathogenic according to our data. Variant chr16-173229-T-C is described in ClinVar as [Likely_pathogenic]. Clinvar id is 15669.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HBA2	NM_000517.6	c.200T>C	p.Leu67Pro	missense_variant	Exon 2 of 3	ENST00000251595.11	NP_000508.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HBA2	ENST00000251595.11	c.200T>C	p.Leu67Pro	missense_variant	Exon 2 of 3	1	NM_000517.6	ENSP00000251595.6

Frequencies

GnomAD3 genomes Cov.: 20

GnomAD4 exome Cov.: 19

GnomAD4 genome Cov.: 20

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:2 Other:1

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

alpha Thalassemia Pathogenic:1

Aug 22, 2024

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

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant summary: HBA2 c.200T>C (p.Leu67Pro), also known as Hb Dartmouth, results in a non-conservative amino acid change in the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant was absent in 133748 control chromosomes (gnomAD). c.200T>C has been reported in the literature in individuals affected with Hb H disease with severe anemia that required transfusions. One pair of twins was heterozygous with the variant and a southeast asian deletion of HBA1 and HBA2 in trans (McBride_2001), while another case was homozygous for the variant without an HBA1 variant reported (Farashi_2015). These data indicate that the variant is likely to be associated with disease. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. The following publications have been ascertained in the context of this evaluation (PMID: 11791870, 25976777). ClinVar contains an entry for this variant (Variation ID: 15669). Based on the evidence outlined above, the variant was classified as likely pathogenic. -

not provided Pathogenic:1

Apr 08, 2024

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The Hb Dartmouth variant (HBA2: c.200T>C; p.Leu67Pro, also known as Leu66Pro when numbered from the mature protein, rs41323248, HbVar ID: 916, ClinVar ID: 15669) is reported heterozygous in individuals with hypochromic microcytic anemia or silent carriers (Farashi 2015, Lorey 2001, McBride 2001). Hb Dartmouth has also been found homozygous or compound heterozygous with a deletion of the entire alpha globin gene cluster in individuals with Hb H disease (Farashi 2015, Lorey 2001, McBride 2001). This variant is believed to be hyper- unstable due to the absence of any detectable abnormal hemoglobin (McBride 2001). This variant is absent from the Genome Aggregation Database (v2.1.1), indicating it is not a common polymorphism. Computational analyses predict that this variant is deleterious (REVEL: 0.897). Based on available information, this variant is considered to be pathogenic. References: Link to HbVar database: https://globin.bx.psu.edu/hbvar/menu.html Farashi S et al. Hb Dartmouth (HBA2: c.200T>C): An a2-Globin Gene Associated with Hb H Disease in One Homozygous Patient. Hemoglobin. 2015;39(3):152-5. PMID: 25976777. Lorey F et al. Hb H hydrops foetalis syndrome: a case report and review of literature. Br J Haematol. 2001 Oct;115(1):72-8. PMID: 11722414. McBride KL et al. Hb Dartmouth [alpha66(E15)Leu-->Pro (alpha2) (CTG-->CCG)]: a novel alpha2-globin gene mutation associated with severe neonatal anemia when inherited in trans with Southeast Asian alpha-thalassemia-1. Hemoglobin. 2001 Nov;25(4):375-82. PMID: 11791870. -

HEMOGLOBIN DARTMOUTH Other:1

Oct 13, 2016

OMIM

Significance: other

Review Status: no assertion criteria provided

Collection Method: literature only

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.54	D
BayesDel_noAF	Pathogenic	0.54
CADD	Uncertain	24
DANN	Uncertain	1.0
DEOGEN2	Benign	0.19	.;T
Eigen	Uncertain	0.40
Eigen_PC	Benign	0.17
FATHMM_MKL	Benign	0.72	D
M_CAP	Pathogenic	0.93	D
MetaRNN	Pathogenic	0.99	D;D
MetaSVM	Pathogenic	1.1	D
PhyloP100		7.5
PrimateAI	Uncertain	0.74	T
PROVEAN	Pathogenic	-6.1	D;D
REVEL	Pathogenic	0.90
Sift	Pathogenic	0.0	D;D
Sift4G	Pathogenic	0.0010	D;D
Vest4		0.95
MutPred		0.94		Loss of stability (P = 0.0062);.;
MVP		1.0
MPC		3.2
ClinPred		1.0	D
GERP RS		4.2
PromoterAI		-0.019	Neutral
gMVP		0.98
Mutation Taster		=12/88	disease causing

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

Other links and lift over

dbSNP: rs41323248; hg19: chr16-223228;