6-75817498-C-G
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 0P and 1B. BS1_Supporting
The NM_004999.4(MYO6):c.-47-3C>G variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000176 in 1,366,502 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 predicting alterations to normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_004999.4 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MYO6 | NM_004999.4 | c.-47-3C>G | splice_region_variant, intron_variant | ENST00000369977.8 | NP_004990.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MYO6 | ENST00000369977.8 | c.-47-3C>G | splice_region_variant, intron_variant | 1 | NM_004999.4 | ENSP00000358994.3 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152108Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000677 AC: 17AN: 251254Hom.: 0 AF XY: 0.0000515 AC XY: 7AN XY: 135802
GnomAD4 exome AF: 0.0000165 AC: 20AN: 1214394Hom.: 0 Cov.: 17 AF XY: 0.0000130 AC XY: 8AN XY: 617044
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152108Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74316
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Oct 23, 2023 | In silico analysis supports a deleterious effect on splicing; Has not been previously published as pathogenic or benign to our knowledge - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at