rs190342289
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_002471.4(MYH6):c.2430-14C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000424 in 1,614,126 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_002471.4 intron
Scores
Clinical Significance
Conservation
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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.2430-14C>T | intron_variant | Intron 20 of 38 | ENST00000405093.9 | NP_002462.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00108 AC: 164AN: 152230Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000551 AC: 138AN: 250562Hom.: 2 AF XY: 0.000583 AC XY: 79AN XY: 135454
GnomAD4 exome AF: 0.000356 AC: 520AN: 1461778Hom.: 5 Cov.: 33 AF XY: 0.000384 AC XY: 279AN XY: 727178
GnomAD4 genome AF: 0.00108 AC: 165AN: 152348Hom.: 0 Cov.: 32 AF XY: 0.00106 AC XY: 79AN XY: 74502
ClinVar
Submissions by phenotype
not specified Benign:4
c.2430-14C>T in intron 20 of MYH6: 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. It has bee n identified in 0.2% (11/4406) of African American chromosomes by the NHLBI Exom e Sequencing Project (http://evs.gs.washington.edu/EVS; dbSNP rs190342289). -
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. -
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Hypertrophic cardiomyopathy 14 Benign:1
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not provided Benign:1
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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