rs138001307
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BS1_SupportingBS2
The NM_001145809.2(MYH14):c.526G>A(p.Ala176Thr) variant causes a missense change. The variant allele was found at a frequency of 0.000208 in 1,613,914 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001145809.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MYH14 | NM_001145809.2 | c.526G>A | p.Ala176Thr | missense_variant | Exon 3 of 43 | ENST00000642316.2 | NP_001139281.1 | |
MYH14 | NM_001077186.2 | c.526G>A | p.Ala176Thr | missense_variant | Exon 3 of 42 | NP_001070654.1 | ||
MYH14 | NM_024729.4 | c.526G>A | p.Ala176Thr | missense_variant | Exon 3 of 41 | NP_079005.3 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000138 AC: 21AN: 152220Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000173 AC: 43AN: 248994Hom.: 0 AF XY: 0.000155 AC XY: 21AN XY: 135098
GnomAD4 exome AF: 0.000216 AC: 315AN: 1461576Hom.: 0 Cov.: 33 AF XY: 0.000212 AC XY: 154AN XY: 727082
GnomAD4 genome AF: 0.000138 AC: 21AN: 152338Hom.: 0 Cov.: 32 AF XY: 0.000134 AC XY: 10AN XY: 74494
ClinVar
Submissions by phenotype
not provided Uncertain:2Benign:2
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This variant is associated with the following publications: (PMID: 27610647) -
The p.Ala176Thr variant has not been reported in the medical literature, and is not listed in gene-specific variant databases. It has been previously identified in our laboratory in an individual with suspected sensorineural hearing loss. The p.Ala176Thr variant is listed in the Genome Aggregation Database (gnomAD) browser with an allele frequency of 0.028% in the non-Finnish European population (identified in 31 out of 111,448 chromosomes), and is classified as a variant of uncertain significance in ClinVar (Variant ID: 228878). The alanine at codon 176 is highly conserved considering 7 species up to cow (Alamut software v2.9.0), and computational analyses suggest that this variant affects the MYH14 protein structure/function (SIFT: damaging, PolyPhen2: probably damaging, MutationTaster: disease causing). Based on the available information, the clinical significance of the p.Ala176Thr variant cannot be determined with certainty. -
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Autosomal dominant nonsyndromic hearing loss 4A Pathogenic:1Uncertain:2
Pathogenic by Deafness Variatiob Database based on PMID: 27610647 -
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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, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease. -
not specified Uncertain:2
Variant summary: MYH14 c.526G>A (p.Ala176Thr) results in a non-conservative amino acid change located in the Myosin head, motor domain (IPR001609) of the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 0.00017 in 248994 control chromosomes (gnomAD). c.526G>A has been reported in the literature in at least one individual affected with Deafness, Autosomal Dominant 4 (Chen_2016). The report does not provide unequivocal conclusions about association of the variant with Deafness, Autosomal Dominant 4. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. The following publications have been ascertained in the context of this evaluation (PMID: 27610647, 34681017). ClinVar contains an entry for this variant (Variation ID: 228878). Based on the evidence outlined above, the variant was classified as uncertain significance. -
The p.Ala176Thr variant in MYH14 has not been previously reported in individuals with hearing loss. This variant has been identified in 0.03% 18/67222 European chromosomes by the Exome Aggregation Consortium (ExAC, http://exac.broadinstitu te.org; dbSNP rs138001307). Although this variant has been seen in the general p opulation, its frequency is not high enough to rule out a pathogenic role. Compu tational prediction tools and conservation analyses suggest that the p.Ala176Thr variant may impact the protein, though this information is not predictive enoug h to determine pathogenicity. In summary, the clinical significance of the p.Ala 176Thr variant is uncertain. -
Meniere disease Uncertain:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at