rs187670753
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_ModerateBP6_ModerateBS1BS2
The NM_001145809.2(MYH14):c.-13C>T variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00114 in 152,338 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_001145809.2 5_prime_UTR_premature_start_codon_gain
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MYH14 | NM_001145809.2 | c.-13C>T | 5_prime_UTR_premature_start_codon_gain_variant | Exon 1 of 43 | ENST00000642316.2 | NP_001139281.1 | ||
MYH14 | NM_001145809.2 | c.-13C>T | 5_prime_UTR_variant | Exon 1 of 43 | ENST00000642316.2 | NP_001139281.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MYH14 | ENST00000642316 | c.-13C>T | 5_prime_UTR_premature_start_codon_gain_variant | Exon 1 of 43 | NM_001145809.2 | ENSP00000493594.1 | ||||
MYH14 | ENST00000642316 | c.-13C>T | 5_prime_UTR_variant | Exon 1 of 43 | NM_001145809.2 | ENSP00000493594.1 |
Frequencies
GnomAD3 genomes AF: 0.00115 AC: 175AN: 152224Hom.: 5 Cov.: 32
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 264Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 212
GnomAD4 genome AF: 0.00114 AC: 173AN: 152338Hom.: 5 Cov.: 32 AF XY: 0.00138 AC XY: 103AN XY: 74482
ClinVar
Submissions by phenotype
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 benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at