rs34536353
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_000519.4(HBD):c.350G>A(p.Arg117His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000273 in 1,613,828 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as other (no stars). 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. R117C) has been classified as Likely benign.
Frequency
Consequence
NM_000519.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HBD | NM_000519.4 | c.350G>A | p.Arg117His | missense_variant | 3/3 | ENST00000650601.1 | NP_000510.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HBD | ENST00000650601.1 | c.350G>A | p.Arg117His | missense_variant | 3/3 | NM_000519.4 | ENSP00000497529.1 | |||
HBD | ENST00000643122.1 | c.350G>A | p.Arg117His | missense_variant | 4/4 | ENSP00000494708.1 | ||||
HBD | ENST00000417377.1 | c.127G>A | p.Ala43Thr | missense_variant | 2/2 | 3 | ENSP00000414741.1 | |||
HBD | ENST00000292901.7 | c.316-260G>A | intron_variant | 3 | ENSP00000292901.3 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152100Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 251170Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135736
GnomAD4 exome AF: 0.0000253 AC: 37AN: 1461728Hom.: 0 Cov.: 32 AF XY: 0.0000303 AC XY: 22AN XY: 727182
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152100Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74302
ClinVar
Submissions by phenotype
HEMOGLOBIN A(2) COBURG Other:1
other, no assertion criteria provided | literature only | OMIM | Dec 12, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at