rs200566974
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001145809.2(MYH14):c.5644G>A(p.Ala1882Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000682 in 1,613,542 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar 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 -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MYH14 | NM_001145809.2 | c.5644G>A | p.Ala1882Thr | missense_variant | 40/43 | ENST00000642316.2 | |
MYH14 | NM_001077186.2 | c.5545G>A | p.Ala1849Thr | missense_variant | 39/42 | ||
MYH14 | NM_024729.4 | c.5521G>A | p.Ala1841Thr | missense_variant | 38/41 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MYH14 | ENST00000642316.2 | c.5644G>A | p.Ala1882Thr | missense_variant | 40/43 | NM_001145809.2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152210Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000162 AC: 4AN: 247504Hom.: 0 AF XY: 0.0000223 AC XY: 3AN XY: 134410
GnomAD4 exome AF: 0.00000547 AC: 8AN: 1461214Hom.: 0 Cov.: 31 AF XY: 0.00000550 AC XY: 4AN XY: 726866
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152328Hom.: 0 Cov.: 32 AF XY: 0.0000268 AC XY: 2AN XY: 74488
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 | Jul 20, 2017 | The p.Ala1882Thr variant in MYH14 has not been previously reported in individual s with hearing loss, but has been identified in 3/30662 South Asian chromosomes by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org; db SNP rs200566974). Although this variant has been seen in the general population, its frequency is not high enough to rule out a pathogenic role. Computational p rediction tools and conservation analysis do not provide strong support for or a gainst an impact to the protein. In summary, the clinical significance of the p. Ala1882Thr variant is uncertain. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at