chr16-176955-A-T
Variant summary
Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PM1PM2PP3_Strong
The NM_000558.5(HBA1):c.122A>T(p.Lys41Met) 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. 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. K41E) has been classified as Uncertain significance.
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.122A>T | p.Lys41Met | missense_variant | 2/3 | ENST00000320868.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HBA1 | ENST00000320868.9 | c.122A>T | p.Lys41Met | missense_variant | 2/3 | 1 | NM_000558.5 | P1 | |
HBA1 | ENST00000472694.1 | n.258A>T | non_coding_transcript_exon_variant | 1/2 | 1 | ||||
HBA1 | ENST00000487791.1 | n.91A>T | non_coding_transcript_exon_variant | 2/2 | 1 | ||||
HBA1 | ENST00000397797.1 | c.26A>T | p.Lys9Met | missense_variant | 2/3 | 2 |
Frequencies
GnomAD3 genomes Cov.: 30
GnomAD4 exome Cov.: 14
GnomAD4 genome Cov.: 30
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at