19-50293587-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PP3_ModerateBS2
The NM_001145809.2(MYH14):c.5369G>A(p.Arg1790His) variant causes a missense change. The variant allele was found at a frequency of 0.0000118 in 1,613,046 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 (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R1790C) has been classified as Uncertain significance.
Frequency
Consequence
NM_001145809.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MYH14 | NM_001145809.2 | c.5369G>A | p.Arg1790His | missense_variant | 39/43 | ENST00000642316.2 | |
MYH14 | NM_001077186.2 | c.5270G>A | p.Arg1757His | missense_variant | 38/42 | ||
MYH14 | NM_024729.4 | c.5246G>A | p.Arg1749His | missense_variant | 37/41 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MYH14 | ENST00000642316.2 | c.5369G>A | p.Arg1790His | missense_variant | 39/43 | NM_001145809.2 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152144Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000402 AC: 1AN: 248900Hom.: 0 AF XY: 0.00000741 AC XY: 1AN XY: 134916
GnomAD4 exome AF: 0.0000123 AC: 18AN: 1460902Hom.: 0 Cov.: 32 AF XY: 0.0000124 AC XY: 9AN XY: 726706
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152144Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74330
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Jan 22, 2015 | The p.Arg1790His variant in MYH14 has not been previously reported in individual s with hearing loss, but has been identified in 1/66722 European chromosomes by the Exome Aggregation Consortium (ExAC, http://exac.broadinstitute.org). Computa tional prediction tools and conservation analysis suggest that this variant may impact the protein, though this information is not predictive enough to determin e pathogenicity. In summary, the clinical significance of the p.Arg1790His varia nt is uncertain. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at