11-77142701-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_000260.4(MYO7A):c.19-8G>A variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000636 in 1,603,424 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, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MYO7A | NM_000260.4 | c.19-8G>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000409709.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MYO7A | ENST00000409709.9 | c.19-8G>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_000260.4 | ||||
MYO7A | ENST00000409619.6 | c.-15-8G>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | |||||
MYO7A | ENST00000458637.6 | c.19-8G>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | P1 | ||||
MYO7A | ENST00000660626.1 | c.109-8G>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152138Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000855 AC: 20AN: 233858Hom.: 0 AF XY: 0.000111 AC XY: 14AN XY: 126624
GnomAD4 exome AF: 0.0000689 AC: 100AN: 1451286Hom.: 0 Cov.: 30 AF XY: 0.0000888 AC XY: 64AN XY: 720836
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152138Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74316
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 26, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at