chr14-23389062-AG-A
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP6BA1
The NM_002471.4(MYH6):c.3979-8delC variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. 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 |
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MYH6 | NM_002471.4 | c.3979-8delC | splice_region_variant, intron_variant | Intron 28 of 38 | ENST00000405093.9 | NP_002462.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.353 AC: 40782AN: 115534Hom.: 8236 Cov.: 0
GnomAD3 exomes AF: 0.320 AC: 44689AN: 139674Hom.: 4831 AF XY: 0.320 AC XY: 24389AN XY: 76278
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.308 AC: 297903AN: 966060Hom.: 26611 Cov.: 0 AF XY: 0.307 AC XY: 147489AN XY: 479754
GnomAD4 genome AF: 0.353 AC: 40854AN: 115646Hom.: 8254 Cov.: 0 AF XY: 0.345 AC XY: 19621AN XY: 56834
ClinVar
Submissions by phenotype
not specified Benign:4Other:1
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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. -
Cardiomyopathy Benign:2
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Dilated Cardiomyopathy, Dominant Uncertain:1
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Atrial septal defect Uncertain:1
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Hypertrophic cardiomyopathy Uncertain:1
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Hypertrophic cardiomyopathy 14 Benign:1
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Cardiovascular phenotype Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Hypertrophic cardiomyopathy 2 Other:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at