rs35317336
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 6P and 8B. PM2PP3_StrongBP6_Very_Strong
The NM_000558.5(HBA1):c.163C>G(p.Gln55Glu) variant causes a missense change involving the alteration of a non-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 Likely benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. Q55R) has been classified as Likely benign.
Frequency
Consequence
NM_000558.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HBA1 | NM_000558.5 | c.163C>G | p.Gln55Glu | missense_variant | 2/3 | ENST00000320868.9 | NP_000549.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HBA1 | ENST00000320868.9 | c.163C>G | p.Gln55Glu | missense_variant | 2/3 | 1 | NM_000558.5 | ENSP00000322421.5 | ||
HBA1 | ENST00000472694.1 | n.299C>G | non_coding_transcript_exon_variant | 1/2 | 1 | |||||
HBA1 | ENST00000487791.1 | n.132C>G | non_coding_transcript_exon_variant | 2/2 | 1 | |||||
HBA1 | ENST00000397797.1 | c.67C>G | p.Gln23Glu | missense_variant | 2/3 | 2 | ENSP00000380899.1 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD4 exome Cov.: 16
GnomAD4 genome Cov.: 31
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Quest Diagnostics Nichols Institute San Juan Capistrano | Dec 29, 2020 | - - |
Benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Dec 15, 2021 | - - |
HEMOGLOBIN J (MEXICO) Other:1
other, no assertion criteria provided | literature only | OMIM | Jul 20, 2016 | - - |
HEMOGLOBIN MEXICO Other:1
other, no assertion criteria provided | literature only | OMIM | Jul 20, 2016 | - - |
HEMOGLOBIN J (PARIS 2) Other:1
other, no assertion criteria provided | literature only | OMIM | Jul 20, 2016 | - - |
HEMOGLOBIN UPPSALA Other:1
other, no assertion criteria provided | literature only | OMIM | Jul 20, 2016 | - - |
HEMOGLOBIN J Other:1
other, no assertion criteria provided | literature only | OMIM | Jul 20, 2016 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at