rs80050551
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_002473.6(MYH9):c.5781G>T(p.Pro1927Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00481 in 1,611,586 control chromosomes in the GnomAD database, including 302 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_002473.6 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MYH9 | NM_002473.6 | c.5781G>T | p.Pro1927Pro | synonymous_variant | Exon 41 of 41 | ENST00000216181.11 | NP_002464.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0249 AC: 3784AN: 151898Hom.: 160 Cov.: 32
GnomAD3 exomes AF: 0.00671 AC: 1658AN: 247134Hom.: 63 AF XY: 0.00488 AC XY: 653AN XY: 133886
GnomAD4 exome AF: 0.00271 AC: 3949AN: 1459570Hom.: 141 Cov.: 31 AF XY: 0.00240 AC XY: 1740AN XY: 726170
GnomAD4 genome AF: 0.0250 AC: 3799AN: 152016Hom.: 161 Cov.: 32 AF XY: 0.0236 AC XY: 1756AN XY: 74350
ClinVar
Submissions by phenotype
not specified Benign:5
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Pro1927Pro in Exon 41 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 7.9% (296/3738) of A frican American chromosomes from a broad population by the NHLBI Exome Sequencin g Project (http://evs.gs.washington.edu/EVS; dbSNP rs80050551). -
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
not provided Benign:3
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Autosomal dominant nonsyndromic hearing loss 17 Benign:1
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases was too high to be consistent with this variant causing disease. Therefore, this variant is classified as benign. -
Atypical hemolytic-uremic syndrome Benign:1
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MYH9-related disorder Benign:1
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases was too high to be consistent with this variant causing disease. Therefore, this variant is classified as benign. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at