rs63750566
Variant summary
Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PM2PM5PP3_Strong
The NM_000558.5(HBA1):c.359C>T(p.Pro120Leu) variant causes a missense change. The variant allele was found at a frequency of 0.00000186 in 1,613,272 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P120S) has been classified as Pathogenic.
Frequency
Consequence
NM_000558.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HBA1 | NM_000558.5 | c.359C>T | p.Pro120Leu | missense_variant | 3/3 | ENST00000320868.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HBA1 | ENST00000320868.9 | c.359C>T | p.Pro120Leu | missense_variant | 3/3 | 1 | NM_000558.5 | P1 | |
HBA1 | ENST00000472694.1 | n.495C>T | non_coding_transcript_exon_variant | 2/2 | 1 | ||||
ENST00000702457.1 | n.150G>A | non_coding_transcript_exon_variant | 1/1 | ||||||
HBA1 | ENST00000397797.1 | c.263C>T | p.Pro88Leu | missense_variant | 3/3 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152204Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000404 AC: 1AN: 247222Hom.: 0 AF XY: 0.00000745 AC XY: 1AN XY: 134242
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461068Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 726818
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152204Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74358
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at