ClinVar Miner

Submissions for variant NM_000260.4(MYO7A):c.3415G>A (p.Gly1139Ser)

gnomAD frequency: 0.00034  dbSNP: rs200840044
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Total submissions: 8
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Illumina Laboratory Services, Illumina RCV000302453 SCV000374341 uncertain significance Usher syndrome type 1 2018-01-13 criteria provided, single submitter clinical testing 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.
Illumina Laboratory Services, Illumina RCV000359563 SCV000374342 likely benign Autosomal dominant nonsyndromic hearing loss 11 2018-01-13 criteria provided, single submitter clinical testing 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.
Illumina Laboratory Services, Illumina RCV000271790 SCV000374343 uncertain significance Autosomal recessive nonsyndromic hearing loss 2 2018-01-13 criteria provided, single submitter clinical testing 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.
Invitae RCV001039078 SCV001202589 likely benign not provided 2024-01-29 criteria provided, single submitter clinical testing
GeneDx RCV001039078 SCV001773600 uncertain significance not provided 2019-07-19 criteria provided, single submitter clinical testing In silico analysis, which includes protein predictors and evolutionary conservation, supports that this variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge
Breda Genetics srl RCV000271790 SCV001961006 uncertain significance Autosomal recessive nonsyndromic hearing loss 2 2021-02-03 criteria provided, single submitter clinical testing The variant in c.3415G>A (p.Gly1139Ser) the MYO7A gene is reported with conflicting interpretation of pathogenicity for usher syndrome type 1, autosomal recessive deafness 2, and autosomal dominant deafness 11 in ClinVar (Variation ID: 306182). The variant is reported with an estimated allele frequency of 0.0000262 in gnomAD exomes and 0.0003 in gnomAD genomes, with no homozygous individuals reported. The nucleotide position is conserved across 35 mammalian species (GERP RS: 5.02). In silico analysis gives inconsistent results.
Ambry Genetics RCV003298369 SCV004002260 uncertain significance Inborn genetic diseases 2023-04-19 criteria provided, single submitter clinical testing The c.3415G>A (p.G1139S) alteration is located in exon 27 (coding exon 26) of the MYO7A gene. This alteration results from a G to A substitution at nucleotide position 3415, causing the glycine (G) at amino acid position 1139 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.
Natera, Inc. RCV001828314 SCV002086666 uncertain significance Usher syndrome type 1B 2019-11-11 no assertion criteria provided clinical testing

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