rs61363656
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001382347.1(MYO5A):c.456-4A>G 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 0.0525 in 1,613,504 control chromosomes in the GnomAD database, including 2,705 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_001382347.1 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MYO5A | NM_001382347.1 | c.456-4A>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000399233.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MYO5A | ENST00000399233.7 | c.456-4A>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 5 | NM_001382347.1 |
Frequencies
GnomAD3 genomes ? AF: 0.0509 AC: 7741AN: 152090Hom.: 273 Cov.: 32
GnomAD3 exomes AF: 0.0614 AC: 15233AN: 248056Hom.: 627 AF XY: 0.0601 AC XY: 8090AN XY: 134546
GnomAD4 exome AF: 0.0526 AC: 76911AN: 1461296Hom.: 2433 Cov.: 31 AF XY: 0.0530 AC XY: 38506AN XY: 726940
GnomAD4 genome ? AF: 0.0508 AC: 7735AN: 152208Hom.: 272 Cov.: 32 AF XY: 0.0534 AC XY: 3974AN XY: 74418
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 12, 2018 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Griscelli syndrome type 1 Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Sep 05, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at