rs281864882
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM1PP3_Strong
The NM_000517.6(HBA2):c.298A>G(p.Lys100Glu) variant causes a missense, splice region change. In-silico tool predicts a pathogenic outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. 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. K100N) has been classified as Likely benign.
Frequency
Consequence
NM_000517.6 missense, splice_region
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 | UniProt |
---|---|---|---|---|---|---|---|
HBA2 | NM_000517.6 | c.298A>G | p.Lys100Glu | missense_variant, splice_region_variant | 2/3 | ENST00000251595.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HBA2 | ENST00000484216.1 | c.268A>G | p.Lys90Glu | missense_variant | 2/2 | 1 | |||
HBA2 | ENST00000251595.11 | c.298A>G | p.Lys100Glu | missense_variant, splice_region_variant | 2/3 | 1 | NM_000517.6 | P1 | |
HBA2 | ENST00000482565.1 | n.434A>G | splice_region_variant, non_coding_transcript_exon_variant | 1/2 | 1 | ||||
HBA2 | ENST00000397806.1 | c.202A>G | p.Lys68Glu | missense_variant, splice_region_variant | 2/3 | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 24
GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0AN: 1432648Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 712854
GnomAD4 genome ? Cov.: 24
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at