rs727505302
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_005379.4(MYO1A):c.1333-8C>T 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 0.0000676 in 1,611,326 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_005379.4 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MYO1A | NM_005379.4 | c.1333-8C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000300119.8 | |||
MYO1A | NM_001256041.2 | c.1333-8C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ||||
MYO1A | XM_011538373.3 | c.1333-8C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ||||
MYO1A | XM_047428876.1 | c.1333-8C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MYO1A | ENST00000300119.8 | c.1333-8C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_005379.4 | P1 | |||
MYO1A | ENST00000442789.6 | c.1333-8C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | P1 | ||||
MYO1A | ENST00000554234.5 | c.847-8C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, NMD_transcript_variant | 5 | |||||
MYO1A | ENST00000476795.1 | n.230-8C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000394 AC: 6AN: 152128Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000163 AC: 4AN: 245142Hom.: 0 AF XY: 0.00000755 AC XY: 1AN XY: 132510
GnomAD4 exome AF: 0.0000706 AC: 103AN: 1459198Hom.: 0 Cov.: 32 AF XY: 0.0000648 AC XY: 47AN XY: 725710
GnomAD4 genome ? AF: 0.0000394 AC: 6AN: 152128Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74318
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 | Oct 19, 2014 | c.1333-8C>T in intron 15 of MYO1A: This variant is not expected to have clinical significance because a C>T change at this position does not diverge from the sp lice consensus sequence and is therefore unlikely to impact splicing. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at