rs2071151
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBP6_Very_Strong
The NM_000260.4(MYO7A):c.1004-35C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.099 ( 992 hom., cov: 31)
Exomes 𝑓: 0.089 ( 8793 hom. )
Failed GnomAD Quality Control
Consequence
MYO7A
NM_000260.4 intron
NM_000260.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0520
Genes affected
MYO7A (HGNC:7606): (myosin VIIA) This gene is a member of the myosin gene family. Myosins are mechanochemical proteins characterized by the presence of a motor domain, an actin-binding domain, a neck domain that interacts with other proteins, and a tail domain that serves as an anchor. This gene encodes an unconventional myosin with a very short tail. Defects in this gene are associated with the mouse shaker-1 phenotype and the human Usher syndrome 1B which are characterized by deafness, reduced vestibular function, and (in human) retinal degeneration. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BP6
?
Variant 11-77159412-C-G is Benign according to our data. Variant chr11-77159412-C-G is described in ClinVar as [Benign]. Clinvar id is 255659.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-77159412-C-G is described in Lovd as [Benign].
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MYO7A | NM_000260.4 | c.1004-35C>G | intron_variant | ENST00000409709.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MYO7A | ENST00000409709.9 | c.1004-35C>G | intron_variant | 1 | NM_000260.4 | ||||
MYO7A | ENST00000409619.6 | c.971-35C>G | intron_variant | 1 | |||||
MYO7A | ENST00000458637.6 | c.1004-35C>G | intron_variant | 1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00 AC: 14976AN: 151056Hom.: 988 Cov.: 31 FAILED QC
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GnomAD3 exomes AF: 0.0992 AC: 23684AN: 238868Hom.: 1817 AF XY: 0.0936 AC XY: 12188AN XY: 130242
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0886 AC: 93178AN: 1051362Hom.: 8793 Cov.: 21 AF XY: 0.0866 AC XY: 46742AN XY: 539900
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GnomAD4 genome ? Data not reliable, filtered out with message: AS_VQSR AF: 0.0992 AC: 14995AN: 151172Hom.: 992 Cov.: 31 AF XY: 0.0997 AC XY: 7361AN XY: 73832
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ClinVar
Significance: Benign
Submissions summary: Benign:5
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Autosomal recessive nonsyndromic hearing loss 2 Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 01, 2021 | - - |
Autosomal dominant nonsyndromic hearing loss 11 Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 01, 2021 | - - |
Usher syndrome type 1 Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 01, 2021 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 14, 2018 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at