rs397516288
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Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 2P and 10B. PM2BP4_ModerateBP6_Very_Strong
The NM_000260.4(MYO7A):c.1821G>A(p.Ser607=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000603 in 1,559,120 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 0.000098 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000056 ( 0 hom. )
Consequence
MYO7A
NM_000260.4 synonymous
NM_000260.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.861
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 -8 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.36).
BP6
?
Variant 11-77172771-G-A is Benign according to our data. Variant chr11-77172771-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 43157.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MYO7A | NM_000260.4 | c.1821G>A | p.Ser607= | synonymous_variant | 16/49 | ENST00000409709.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MYO7A | ENST00000409709.9 | c.1821G>A | p.Ser607= | synonymous_variant | 16/49 | 1 | NM_000260.4 | ||
MYO7A | ENST00000458637.6 | c.1821G>A | p.Ser607= | synonymous_variant | 16/49 | 1 | P1 | ||
MYO7A | ENST00000409619.6 | c.1788G>A | p.Ser596= | synonymous_variant | 17/50 | 1 | |||
MYO7A | ENST00000669443.1 | c.186G>A | p.Ser62= | synonymous_variant | 3/3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000986 AC: 15AN: 152196Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000541 AC: 9AN: 166424Hom.: 0 AF XY: 0.0000451 AC XY: 4AN XY: 88706
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GnomAD4 exome AF: 0.0000562 AC: 79AN: 1406806Hom.: 0 Cov.: 31 AF XY: 0.0000518 AC XY: 36AN XY: 694696
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GnomAD4 genome ? AF: 0.0000985 AC: 15AN: 152314Hom.: 0 Cov.: 33 AF XY: 0.0000940 AC XY: 7AN XY: 74482
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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 | Aug 17, 2010 | Ser607Ser in exon 16 of MYO7A: This variant is not expected to have clinical sig nificance because it does not alter an amino acid residue and is not located nea r a splice junction. - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 25, 2024 | - - |
Computational scores
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Name
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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