11-77156908-C-T
Variant summary
Our verdict is Benign. The variant received -15 ACMG points: 0P and 15B. BP4_ModerateBP6_Very_StrongBP7BS1
The NM_000260.4(MYO7A):c.639C>T(p.Phe213Phe) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000911 in 1,614,020 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 Benign (★★).
Frequency
Consequence
NM_000260.4 synonymous
Scores
Clinical Significance
Conservation
Publications
- nonsyndromic genetic hearing lossInheritance: AD Classification: DEFINITIVE Submitted by: ClinGen
- autosomal recessive nonsyndromic hearing loss 2Inheritance: AR Classification: DEFINITIVE, STRONG, MODERATE, LIMITED Submitted by: Labcorp Genetics (formerly Invitae), PanelApp Australia, Ambry Genetics, G2P
- Usher syndrome type 1Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: ClinGen, Orphanet, PanelApp Australia
- Usher syndrome type 1BInheritance: AR Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), G2P
- autosomal dominant nonsyndromic hearing loss 11Inheritance: AD Classification: STRONG, MODERATE Submitted by: Ambry Genetics, PanelApp Australia, Labcorp Genetics (formerly Invitae)
- autosomal dominant nonsyndromic hearing lossInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- hearing loss, autosomal recessiveInheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
- Usher syndrome type 2Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
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ACMG classification
Our verdict: Benign. The variant received -15 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MYO7A | ENST00000409709.9 | c.639C>T | p.Phe213Phe | synonymous_variant | Exon 7 of 49 | 1 | NM_000260.4 | ENSP00000386331.3 | ||
MYO7A | ENST00000458637.6 | c.639C>T | p.Phe213Phe | synonymous_variant | Exon 7 of 49 | 1 | ENSP00000392185.2 | |||
MYO7A | ENST00000409619.6 | c.606C>T | p.Phe202Phe | synonymous_variant | Exon 8 of 50 | 1 | ENSP00000386635.2 |
Frequencies
GnomAD3 genomes AF: 0.000151 AC: 23AN: 152222Hom.: 0 Cov.: 33 show subpopulations
GnomAD2 exomes AF: 0.000441 AC: 110AN: 249172 AF XY: 0.000451 show subpopulations
GnomAD4 exome AF: 0.0000848 AC: 124AN: 1461680Hom.: 0 Cov.: 32 AF XY: 0.0000866 AC XY: 63AN XY: 727124 show subpopulations
Age Distribution
GnomAD4 genome AF: 0.000151 AC: 23AN: 152340Hom.: 0 Cov.: 33 AF XY: 0.000148 AC XY: 11AN XY: 74494 show subpopulations
Age Distribution
ClinVar
Submissions by phenotype
not specified Benign:1
p.Phe213Phe in exon 7 of MYO7A: This variant is not expected to have clinical si gnificance because it does not alter an amino acid residue, is not located withi n the splice consensus sequence, and has been identified in 0.5% (99/18868) East Asian chromosomes by the Genome Aggregation Database (gnomAD, http://gnomad.bro adinstitute.org/; dbSNP rs540197003). -
Usher syndrome type 1B Benign:1
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not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at