chr18-3086031-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_003803.4(MYOM1):c.4251+7G>A variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000026 in 1,538,674 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_003803.4 splice_region, 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 |
---|---|---|---|---|---|---|---|
MYOM1 | NM_003803.4 | c.4251+7G>A | splice_region_variant, intron_variant | ENST00000356443.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MYOM1 | ENST00000356443.9 | c.4251+7G>A | splice_region_variant, intron_variant | 1 | NM_003803.4 | P2 | |||
MYOM1 | ENST00000261606.11 | c.3963+7G>A | splice_region_variant, intron_variant | 1 | A2 | ||||
MYOM1 | ENST00000581075.1 | c.351+7G>A | splice_region_variant, intron_variant, NMD_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000854 AC: 13AN: 152146Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000287 AC: 7AN: 244200Hom.: 0 AF XY: 0.0000301 AC XY: 4AN XY: 132864
GnomAD4 exome AF: 0.0000195 AC: 27AN: 1386528Hom.: 0 Cov.: 22 AF XY: 0.0000173 AC XY: 12AN XY: 693858
GnomAD4 genome ? AF: 0.0000854 AC: 13AN: 152146Hom.: 0 Cov.: 31 AF XY: 0.000108 AC XY: 8AN XY: 74320
ClinVar
Submissions by phenotype
Hypertrophic cardiomyopathy Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 20, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at