rs372741317
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BS1BS2
The NM_001145809.2(MYH14):c.36G>A(p.Lys12Lys) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000177 in 1,578,718 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 Likely benign (★★).
Frequency
Consequence
NM_001145809.2 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MYH14 | NM_001145809.2 | c.36G>A | p.Lys12Lys | synonymous_variant | Exon 2 of 43 | ENST00000642316.2 | NP_001139281.1 | |
MYH14 | NM_001077186.2 | c.36G>A | p.Lys12Lys | synonymous_variant | Exon 2 of 42 | NP_001070654.1 | ||
MYH14 | NM_024729.4 | c.36G>A | p.Lys12Lys | synonymous_variant | Exon 2 of 41 | NP_079005.3 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000960 AC: 146AN: 152154Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000128 AC: 24AN: 187364Hom.: 0 AF XY: 0.000116 AC XY: 12AN XY: 103688
GnomAD4 exome AF: 0.0000925 AC: 132AN: 1426446Hom.: 0 Cov.: 31 AF XY: 0.0000848 AC XY: 60AN XY: 707698
GnomAD4 genome AF: 0.000965 AC: 147AN: 152272Hom.: 0 Cov.: 32 AF XY: 0.000954 AC XY: 71AN XY: 74458
ClinVar
Submissions by phenotype
not provided Benign:2
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Autosomal dominant nonsyndromic hearing loss 4A Benign:1
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease. -
MYH14-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