16-177406-C-G
Variant summary
Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PM1PM2PM5PP3_Moderate
The NM_000558.5(HBA1):c.424C>G(p.Arg142Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000186 in 1,613,554 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as other (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R142C) 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.424C>G | p.Arg142Gly | missense_variant | 3/3 | ENST00000320868.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HBA1 | ENST00000320868.9 | c.424C>G | p.Arg142Gly | missense_variant | 3/3 | 1 | NM_000558.5 | P1 | |
HBA1 | ENST00000472694.1 | n.560C>G | non_coding_transcript_exon_variant | 2/2 | 1 | ||||
ENST00000702457.1 | n.85G>C | non_coding_transcript_exon_variant | 1/1 | ||||||
HBA1 | ENST00000397797.1 | c.328C>G | p.Arg110Gly | missense_variant | 3/3 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152246Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461308Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 726958
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152246Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74386
ClinVar
Submissions by phenotype
HEMOGLOBIN J (CAMAGUEY) Other:1
other, no assertion criteria provided | literature only | OMIM | May 10, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at