16-176796-C-T
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_000558.5(HBA1):c.80C>T(p.Ala27Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000811 in 147,972 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 nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A27E) 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_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HBA1 | NM_000558.5 | c.80C>T | p.Ala27Val | missense_variant | 1/3 | ENST00000320868.9 | NP_000549.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HBA1 | ENST00000320868.9 | c.80C>T | p.Ala27Val | missense_variant | 1/3 | 1 | NM_000558.5 | ENSP00000322421.5 | ||
HBA1 | ENST00000472694.1 | n.99C>T | non_coding_transcript_exon_variant | 1/2 | 1 | |||||
HBA1 | ENST00000487791.1 | n.49C>T | non_coding_transcript_exon_variant | 1/2 | 1 | |||||
HBA1 | ENST00000397797.1 | c.-2+34C>T | intron_variant | 2 | ENSP00000380899.1 |
Frequencies
GnomAD3 genomes AF: 0.0000811 AC: 12AN: 147886Hom.: 0 Cov.: 28
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000353 AC: 5AN: 1415772Hom.: 0 Cov.: 26 AF XY: 0.00000285 AC XY: 2AN XY: 702882
GnomAD4 genome AF: 0.0000811 AC: 12AN: 147972Hom.: 0 Cov.: 28 AF XY: 0.0000694 AC XY: 5AN XY: 72036
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at