rs63751238
Variant summary
Our verdict is Pathogenic. Variant got 14 ACMG points: 14P and 0B. PVS1PM2PP3_Strong
The NM_000517.6(HBA2):c.300+2T>A variant causes a splice donor change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000696 in 1,436,438 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_000517.6 splice_donor
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HBA2 | NM_000517.6 | c.300+2T>A | splice_donor_variant | ENST00000251595.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HBA2 | ENST00000251595.11 | c.300+2T>A | splice_donor_variant | 1 | NM_000517.6 | P1 | |||
HBA2 | ENST00000484216.1 | c.272T>A | p.Val91Glu | missense_variant | 2/2 | 1 | |||
HBA2 | ENST00000482565.1 | n.436+2T>A | splice_donor_variant, non_coding_transcript_variant | 1 | |||||
HBA2 | ENST00000397806.1 | c.204+2T>A | splice_donor_variant | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 24
GnomAD3 exomes AF: 0.00000448 AC: 1AN: 223156Hom.: 0 AF XY: 0.00000811 AC XY: 1AN XY: 123296
GnomAD4 exome AF: 6.96e-7 AC: 1AN: 1436438Hom.: 0 Cov.: 31 AF XY: 0.00000140 AC XY: 1AN XY: 714708
GnomAD4 genome ? Cov.: 24
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at