11-77194455-C-T
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6_Very_StrongBP7
The NM_000260.4(MYO7A):c.4254C>T(p.Pro1418Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000615 in 1,610,654 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_000260.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MYO7A | ENST00000409709.9 | c.4254C>T | p.Pro1418Pro | synonymous_variant | Exon 32 of 49 | 1 | NM_000260.4 | ENSP00000386331.3 | ||
MYO7A | ENST00000458637.6 | c.4254C>T | p.Pro1418Pro | synonymous_variant | Exon 32 of 49 | 1 | ENSP00000392185.2 | |||
MYO7A | ENST00000409619.6 | c.4221C>T | p.Pro1407Pro | synonymous_variant | Exon 33 of 50 | 1 | ENSP00000386635.2 | |||
MYO7A | ENST00000458169.2 | c.1797C>T | p.Pro599Pro | synonymous_variant | Exon 12 of 29 | 1 | ENSP00000417017.2 | |||
MYO7A | ENST00000670577.1 | n.2094C>T | non_coding_transcript_exon_variant | Exon 15 of 32 | ENSP00000499323.1 |
Frequencies
GnomAD3 genomes AF: 0.0000920 AC: 14AN: 152188Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.0000454 AC: 11AN: 242130Hom.: 0 AF XY: 0.0000610 AC XY: 8AN XY: 131252
GnomAD4 exome AF: 0.0000583 AC: 85AN: 1458348Hom.: 1 Cov.: 30 AF XY: 0.0000538 AC XY: 39AN XY: 725032
GnomAD4 genome AF: 0.0000919 AC: 14AN: 152306Hom.: 1 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74472
ClinVar
Submissions by phenotype
not specified Benign:1
p.Pro1418Pro in exon 32 of MYO7A: This variant is not expected to have clinical significance because it does not alter an amino acid residue and is not located within the splice consensus sequence. This variant has been identified in 4/4901 8 European chromosomes by the Exome Aggregation Consortium (ExAC, http://exac.br oadinstitute.org). -
not provided Benign:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at