chr22-36312211-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BS1BS2
The NM_002473.6(MYH9):c.1566G>A(p.Pro522Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000142 in 1,614,014 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_002473.6 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MYH9 | NM_002473.6 | c.1566G>A | p.Pro522Pro | synonymous_variant | Exon 14 of 41 | ENST00000216181.11 | NP_002464.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000552 AC: 84AN: 152104Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000203 AC: 51AN: 250976Hom.: 0 AF XY: 0.000155 AC XY: 21AN XY: 135792
GnomAD4 exome AF: 0.0000985 AC: 144AN: 1461792Hom.: 0 Cov.: 36 AF XY: 0.0000908 AC XY: 66AN XY: 727204
GnomAD4 genome AF: 0.000558 AC: 85AN: 152222Hom.: 0 Cov.: 32 AF XY: 0.000510 AC XY: 38AN XY: 74438
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:2
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not specified Benign:2
p.Pro522Pro in exon 14 of MYH9: This variant is not expected to have clinical si gnificance because it does not alter an amino acid residue, is not located withi n the splice consensus sequence, and has been identified in 0.1% (12/10304) of A frican chromosomes by the Exome Aggregation Consortium (ExAC, http://exac.broadi nstitute.org; dbSNP rs145517108). -
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MYH9-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at