chr13-108806672-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001198950.3(MYO16):c.742-7G>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 0.704 in 1,608,986 control chromosomes in the GnomAD database, including 403,828 homozygotes. 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 Benign (★).
Frequency
Consequence
NM_001198950.3 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MYO16 | NM_001198950.3 | c.742-7G>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000457511.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MYO16 | ENST00000457511.7 | c.742-7G>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_001198950.3 | A2 | |||
MYO16 | ENST00000356711.7 | c.676-7G>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | P2 | ||||
MYO16 | ENST00000251041.10 | c.676-7G>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 5 | |||||
MYO16 | ENST00000375857.6 | n.62-7G>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.638 AC: 96866AN: 151804Hom.: 32696 Cov.: 31
GnomAD3 exomes AF: 0.724 AC: 181411AN: 250636Hom.: 66849 AF XY: 0.727 AC XY: 98499AN XY: 135408
GnomAD4 exome AF: 0.711 AC: 1035864AN: 1457064Hom.: 371108 Cov.: 34 AF XY: 0.714 AC XY: 517378AN XY: 725054
GnomAD4 genome AF: 0.638 AC: 96911AN: 151922Hom.: 32720 Cov.: 31 AF XY: 0.645 AC XY: 47928AN XY: 74276
ClinVar
Submissions by phenotype
MYO16-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 17, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at