16-173480-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 6P and 2B. PM2PP3_StrongBP6_Moderate
The NM_000517.6(HBA2):c.309C>A(p.Ser103Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000686 in 1,458,094 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 Likely benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_000517.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HBA2 | NM_000517.6 | c.309C>A | p.Ser103Arg | missense_variant | 3/3 | ENST00000251595.11 | NP_000508.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HBA2 | ENST00000251595.11 | c.309C>A | p.Ser103Arg | missense_variant | 3/3 | 1 | NM_000517.6 | ENSP00000251595.6 |
Frequencies
GnomAD3 genomes Cov.: 25
GnomAD4 exome AF: 6.86e-7 AC: 1AN: 1458094Hom.: 0 Cov.: 33 AF XY: 0.00000138 AC XY: 1AN XY: 725182
GnomAD4 genome Cov.: 25
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Aug 03, 2021 | - - |
HEMOGLOBIN MANITOBA Other:1
other, no assertion criteria provided | literature only | OMIM | May 21, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at