rs35103459
Positions:
Variant summary
Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PM1PM2PP3_StrongPP5_Moderate
The NM_000184.3(HBG2):c.277C>T(p.His93Tyr) variant causes a missense change involving the alteration of a conserved nucleotide. 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 Pathogenic (★).
Frequency
Genomes: not found (cov: 31)
Consequence
HBG2
NM_000184.3 missense
NM_000184.3 missense
Scores
13
3
2
Clinical Significance
Conservation
PhyloP100: 7.51
Genes affected
HBG2 (HGNC:4832): (hemoglobin subunit gamma 2) The gamma globin genes (HBG1 and HBG2) are normally expressed in the fetal liver, spleen and bone marrow. Two gamma chains together with two alpha chains constitute fetal hemoglobin (HbF) which is normally replaced by adult hemoglobin (HbA) at birth. In some beta-thalassemias and related conditions, gamma chain production continues into adulthood. The two types of gamma chains differ at residue 136 where glycine is found in the G-gamma product (HBG2) and alanine is found in the A-gamma product (HBG1). The former is predominant at birth. 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]
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ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 10 ACMG points.
PM1
In a binding_site proximal binding residue (size 0) in uniprot entity HBG2_HUMAN
PM2
Very rare variant in population databases, with high coverage;
PP3
MetaRNN computational evidence supports a deleterious effect, 0.992
PP5
Variant 11-5254330-G-A is Pathogenic according to our data. Variant chr11-5254330-G-A is described in ClinVar as [Pathogenic]. Clinvar id is 14989.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HBG2 | NM_000184.3 | c.277C>T | p.His93Tyr | missense_variant | 2/3 | ENST00000336906.6 | NP_000175.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HBG2 | ENST00000336906.6 | c.277C>T | p.His93Tyr | missense_variant | 2/3 | 1 | NM_000184.3 | ENSP00000338082 | P1 | |
HBG2 | ENST00000380252.6 | c.112C>T | p.His38Tyr | missense_variant | 2/3 | 3 | ENSP00000369602 | |||
HBG2 | ENST00000444587.1 | c.*146C>T | 3_prime_UTR_variant | 2/3 | 2 | ENSP00000488218 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD3 genomes
Cov.:
31
GnomAD4 exome Cov.: 34
GnomAD4 exome
Cov.:
34
GnomAD4 genome Cov.: 31
GnomAD4 genome
Cov.:
31
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:2
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Cyanosis, transient neonatal Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | May 01, 1989 | - - |
not provided Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | May 18, 2021 | The Hb FM-Fort Ripley variant (HBA1: c.277C>T; p.His93Tyr, also known as His92Tyr when numbered from the mature protein, rs35103459) is reported in the literature in multiple individuals and segregates with disease in large families affected with transient neonatal cyanosis (see link to HbVar, Hain 1994, Hooven 2016, Priest 1989). This variant is also reported in ClinVar (Variation ID: 14989), and is absent from the Genome Aggregation Database, indicating it is not a common polymorphism. The histidine at codon 93 is highly conserved, and computational analyses predict that this variant is deleterious (REVEL: 0.893). Based on available information, this variant is considered to be pathogenic. References: Link to HbVar for Hb FM-Fort Ripley: https://globin.bx.psu.edu/cgi-bin/hbvar/query_vars3?mode=output&display_format=page&i=609 Hain RD et al. Hb FM-Fort Ripley: confirmation of autosomal dominant inheritance and diagnosis by PCR and direct nucleotide sequencing. Hum Mutat. 1994;3(3):239-42. PMID: 7517266. Hooven TA et al. Diagnosis of a rare fetal haemoglobinopathy in the age of next-generation sequencing. BMJ Case Rep. 2016 Apr 19;2016:10.1136/bcr-2016-215193. PMID: 27095814. Priest JR et al. Mutant fetal hemoglobin causing cyanosis in a newborn. Pediatrics. 1989 May;83(5):734-6. PMID: 2470017. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Benign
.;.;T;.
Eigen
Pathogenic
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Pathogenic
D;D;D;D
M_CAP
Pathogenic
D
MetaRNN
Pathogenic
D;D;D;D
MetaSVM
Pathogenic
D
MutationAssessor
Pathogenic
.;.;H;.
MutationTaster
Benign
A;A;A
PROVEAN
Pathogenic
.;.;D;.
REVEL
Pathogenic
Sift
Pathogenic
.;.;D;.
Sift4G
Pathogenic
.;.;D;.
Polyphen
1.0
.;.;D;.
Vest4
0.94
MutPred
Loss of methylation at K96 (P = 0.0606);Loss of methylation at K96 (P = 0.0606);Loss of methylation at K96 (P = 0.0606);.;
MVP
0.98
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at