chr3-38138762-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_002468.5(MYD88):c.62C>G(p.Pro21Arg) variant causes a missense change. The variant allele was found at a frequency of 0.00000205 in 1,460,464 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 Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. P21P) has been classified as Likely benign.
Frequency
Consequence
NM_002468.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MYD88 | NM_002468.5 | c.62C>G | p.Pro21Arg | missense_variant | 1/5 | ENST00000650905.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MYD88 | ENST00000650905.2 | c.62C>G | p.Pro21Arg | missense_variant | 1/5 | NM_002468.5 | A1 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 249044Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135344
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1460464Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2AN XY: 726572
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
Pyogenic bacterial infections due to MyD88 deficiency Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Apr 14, 2021 | In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Class C0"). This variant has not been reported in the literature in individuals with MYD88-related conditions. This variant is present in population databases (rs563686976, ExAC 0.009%). This sequence change replaces proline with arginine at codon 34 of the MYD88 protein (p.Pro34Arg). The proline residue is highly conserved and there is a moderate physicochemical difference between proline and arginine. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at