rs397516334
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Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 2P and 11B. PM2BP4_ModerateBP6_Very_StrongBP7
The NM_000260.4(MYO7A):c.72C>T(p.Ile24=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000093 in 1,612,078 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
Genomes: 𝑓 0.000020 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0000082 ( 0 hom. )
Consequence
MYO7A
NM_000260.4 synonymous
NM_000260.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.474
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 -9 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.22).
BP6
?
Variant 11-77142762-C-T is Benign according to our data. Variant chr11-77142762-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 43341.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-77142762-C-T is described in Lovd as [Benign].
BP7
?
Synonymous conserved (PhyloP=-0.474 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MYO7A | NM_000260.4 | c.72C>T | p.Ile24= | synonymous_variant | 3/49 | ENST00000409709.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MYO7A | ENST00000409709.9 | c.72C>T | p.Ile24= | synonymous_variant | 3/49 | 1 | NM_000260.4 | ||
MYO7A | ENST00000458637.6 | c.72C>T | p.Ile24= | synonymous_variant | 3/49 | 1 | P1 | ||
MYO7A | ENST00000409619.6 | c.39C>T | p.Ile13= | synonymous_variant | 4/50 | 1 | |||
MYO7A | ENST00000660626.1 | c.162C>T | p.Ile54= | synonymous_variant | 2/2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152158Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.00000408 AC: 1AN: 244930Hom.: 0 AF XY: 0.00000751 AC XY: 1AN XY: 133102
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GnomAD4 exome AF: 0.00000822 AC: 12AN: 1459920Hom.: 0 Cov.: 33 AF XY: 0.00000964 AC XY: 7AN XY: 725958
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GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152158Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74322
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ClinVar
Significance: Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Mar 30, 2011 | The Ile24Ile variant in MYO7A has not been reported in the literature nor previo usly identified by our laboratory. This variant is not expected to have clinical significance since it does not alter an amino acid residue and is not located n ear a splice junction. - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jul 08, 2023 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at