chr11-5226997-TCTC-T

Variant names:

• chr11-5226997-TCTC-T
• rs63750928
• NM_000518.5:c.22_24delGAG

Variant summary

Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PM2 PM4_Supporting PP5_Very_Strong

The NM_000518.5(HBB):​c.22_24delGAG​(p.Glu8del) variant causes a conservative inframe deletion change. The variant allele was found at a frequency of 0.00000657 in 152,162 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely pathogenic (★★).

• Frequency:
  • Genomes: 𝑓 0.0000066 (0 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: HBB NM_000518.5 conservative_inframe_deletion
• Clinical Significance: Likely pathogenic criteria provided, multiple submitters, no conflicts P:2 O:1
• Conservation: PhyloP100: 7.13

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 11 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PM4: Nonframeshift variant in NON repetitive region in NM_000518.5. Strenght limited to Supporting due to length of the change: 1aa.
• PP5: Variant 11-5226997-TCTC-T is Pathogenic according to our data. Variant chr11-5226997-TCTC-T is described in ClinVar as [Likely_pathogenic]. Clinvar id is 15247.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
HBB	NM_000518.5	c.22_24delGAG	p.Glu8del	conservative_inframe_deletion	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.22_24delGAG	p.Glu8del	conservative_inframe_deletion	Exon 1 of 3	1	NM_000518.5	ENSP00000333994.3

Frequencies

GnomAD3 genomes AF: 0.00000657 AC: 1 AN: 152162 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000147

Gnomad OTH AF: 0.00

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 1460294 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 726598

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: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.00000657 AC: 1 AN: 152162 Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0 AN XY: 74356

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000147

Gnomad4 OTH AF: 0.00

Bravo AF: 0.00000378

ClinVar

Significance: Likely pathogenic

Submissions summary: Pathogenic:2 Other:1

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Pathogenic:2

Feb 15, 2021

Quest Diagnostics Nichols Institute San Juan Capistrano

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant has been reported to be an unstable hemoglobin variant with slightly increased oxygen affinity. Heterozygosity for Hb Leiden is associated with mild hemolytic anemia and reticulocytosis (PMID 6874375 (1983), 14688008 (2003)). -

Nov 10, 2021

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The Hb Leiden variant (HBB: c.22_24del; p.Glu8del, also known as Glu7del when numbered from the mature protein, rs63750928) is reported in the literature in multiple individuals affected with episodes of hemolytic anemia, although most exhibited normal hematology outside of hemolytic episodes (De Jong 1968, Rieder 1974, Schroeder 1982, HbVar database and references therein). Additionally, this variant has been observed in trans to HbE in a proband with a clinical picture of mild thalassemia intermedia and was absent from both parents, suggesting a de novo origin in this individual (Sanguansermsri 2003). This variant is absent from the Genome Aggregation Database, indicating it is not a common polymorphism. This variant deletes a single glutamate residue, leaving the rest of the protein in-frame. Functional analyses suggest the variant is mildly unstable, although it is unclear if this is clinically significant (Rieder 1974). Still, based on available information, including its occurrence in multiple affected individuals, the Hb Leiden variant is considered to be likely pathogenic. References: HbVar link for Hb Leiden: http://globin.bx.psu.edu/cgi-bin/hbvar/query_vars3?mode=output&display_format=page&i=720 De Jong WW et al. Haemoglobin Leiden: deletion of beta-6 or 7 glutamic acid. Nature. 1968 Nov 23;220(5169):788-90. PMID: 5698750 Rieder RF and James GW. Imbalance in alpha and beta globin synthesis associated with a hemoglobinopathy. J Clin Invest. 1974 Oct;54(4):948-56. PMID: 4430724. Sanguansermsri P et al. Spontaneous mutation of the hemoglobin Leiden (beta 6 or 7 Glu-->0) in a Thai girl. Haematologica. 2003 Dec;88(12):ECR35. PMID: 14688008. Schroeder WA et al. An unusual phenotypic expression of Hb-Leiden. Biochem Genet. 1982 Dec;20(11-12):1175-87. PMID: 7165693. -

HEMOGLOBIN LEIDEN Other:1

Nov 14, 2019

OMIM

Significance: other

Review Status: no assertion criteria provided

Collection Method: literature only

- -

Computational scores

Source: dbNSFP v4.3

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: rs63750928; hg19: chr11-5248227;