rs781886473
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 2P and 12B. PM2BP4_StrongBP6_Very_Strong
The NM_000260.4(MYO7A):c.2094+8G>A variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000372 in 1,611,876 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_000260.4 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MYO7A | NM_000260.4 | c.2094+8G>A | splice_region_variant, intron_variant | ENST00000409709.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MYO7A | ENST00000409709.9 | c.2094+8G>A | splice_region_variant, intron_variant | 1 | NM_000260.4 | ||||
MYO7A | ENST00000409619.6 | c.2061+8G>A | splice_region_variant, intron_variant | 1 | |||||
MYO7A | ENST00000458637.6 | c.2094+8G>A | splice_region_variant, intron_variant | 1 | P1 | ||||
MYO7A | ENST00000409893.6 | c.159+8G>A | splice_region_variant, intron_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152226Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000121 AC: 3AN: 247456Hom.: 0 AF XY: 0.0000149 AC XY: 2AN XY: 134638
GnomAD4 exome AF: 0.00000343 AC: 5AN: 1459650Hom.: 0 Cov.: 34 AF XY: 0.00000413 AC XY: 3AN XY: 725704
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152226Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74362
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Dec 08, 2016 | c.2094+8G>A in intron 17 of MYO7A : This variant is not expected to have clinica l significance because it is not located within the splice consensus sequence. I t has been identified in 1/11464 of Latino chromosomes by the Exome Aggregation Consortium (ExAC, http://exac.broadinstitute.org; dbSNP rs781886473). - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jun 07, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at