16-176746-C-G
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_000558.5(HBA1):c.30C>G(p.Asn10Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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. N10T) has been classified as Likely benign.
Frequency
Consequence
NM_000558.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
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.30C>G | p.Asn10Lys | 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.30C>G | p.Asn10Lys | missense_variant | 1/3 | 1 | NM_000558.5 | ENSP00000322421 | P1 | |
HBA1 | ENST00000472694.1 | n.49C>G | non_coding_transcript_exon_variant | 1/2 | 1 | |||||
HBA1 | ENST00000397797.1 | c.-18C>G | 5_prime_UTR_variant | 1/3 | 2 | ENSP00000380899 | ||||
HBA1 | ENST00000487791.1 | upstream_gene_variant | 1 |
Frequencies
GnomAD3 genomes Cov.: 28
GnomAD4 exome Cov.: 28
GnomAD4 genome Cov.: 28
ClinVar
Submissions by phenotype
HEMOGLOBIN DELFZICHT Other:1
other, no assertion criteria provided | literature only | OMIM | Jul 20, 2016 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at