rs796313537
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP6BS1BS2
The NM_002471.4(MYH6):c.3979-7_3979-6delTC variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000289 in 121,160 control chromosomes in the GnomAD database, with no homozygous occurrence. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_002471.4 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MYH6 | NM_002471.4 | c.3979-7_3979-6delTC | splice_region_variant, intron_variant | Intron 28 of 38 | ENST00000405093.9 | NP_002462.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000289 AC: 35AN: 121102Hom.: 0 Cov.: 26
GnomAD3 exomes AF: 0.0000542 AC: 10AN: 184396Hom.: 0 AF XY: 0.0000396 AC XY: 4AN XY: 101078
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.000618 AC: 880AN: 1424558Hom.: 0 AF XY: 0.000608 AC XY: 430AN XY: 706840
GnomAD4 genome AF: 0.000289 AC: 35AN: 121160Hom.: 0 Cov.: 26 AF XY: 0.000319 AC XY: 19AN XY: 59560
ClinVar
Submissions by phenotype
not specified Uncertain:1
proposed classification - variant undergoing re-assessment, contact laboratory -
Cardiomyopathy Uncertain:1
- -
Hypertrophic cardiomyopathy 14 Benign:1
- -
MYH6-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at