rs63749927
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 5P and 1B. PM1PM2PP3BP6
The NM_000558.5(HBA1):c.362C>A(p.Ala121Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000031 in 1,613,068 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_000558.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HBA1 | NM_000558.5 | c.362C>A | p.Ala121Glu | missense_variant | 3/3 | ENST00000320868.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HBA1 | ENST00000320868.9 | c.362C>A | p.Ala121Glu | missense_variant | 3/3 | 1 | NM_000558.5 | P1 | |
HBA1 | ENST00000472694.1 | n.498C>A | non_coding_transcript_exon_variant | 2/2 | 1 | ||||
ENST00000702457.1 | n.147G>T | non_coding_transcript_exon_variant | 1/1 | ||||||
HBA1 | ENST00000397797.1 | c.266C>A | p.Ala89Glu | missense_variant | 3/3 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152194Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000405 AC: 1AN: 247074Hom.: 0 AF XY: 0.00000745 AC XY: 1AN XY: 134158
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1460874Hom.: 0 Cov.: 32 AF XY: 0.00000413 AC XY: 3AN XY: 726720
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152194Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74348
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:1
Benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Feb 11, 2022 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Quest Diagnostics Nichols Institute San Juan Capistrano | May 09, 2018 | - - |
HEMOGLOBIN J (MEERUT) Other:1
other, no assertion criteria provided | literature only | OMIM | Jul 20, 2016 | - - |
HEMOGLOBIN J (BIRMINGHAM) 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