rs555976716
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_002471.4(MYH6):c.3979-8C>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. 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_002471.4 splice_region, intron
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MYH6 | NM_002471.4 | c.3979-8C>T | splice_region_variant, intron_variant | Intron 28 of 38 | ENST00000405093.9 | NP_002462.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0176 AC: 1146AN: 64966Hom.: 17 Cov.: 0
GnomAD3 exomes AF: 0.00483 AC: 737AN: 152678Hom.: 9 AF XY: 0.00486 AC XY: 406AN XY: 83470
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00502 AC: 2166AN: 431174Hom.: 23 Cov.: 0 AF XY: 0.00576 AC XY: 1213AN XY: 210770
GnomAD4 genome AF: 0.0177 AC: 1148AN: 64952Hom.: 17 Cov.: 0 AF XY: 0.0173 AC XY: 554AN XY: 32112
ClinVar
Submissions by phenotype
not specified Benign:4
- -
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
- -
- -
not provided Benign:2
- -
- -
Hypertrophic cardiomyopathy 14 Benign:1
- -
Dilated cardiomyopathy 1EE;C2750467:Hypertrophic cardiomyopathy 14;C3279790:Atrial septal defect 3;C3279791:Sick sinus syndrome 3, susceptibility to;C3495498:Hypertrophic cardiomyopathy 1 Benign:1
- -
Cardiomyopathy Benign:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at