16-15745246-G-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_002474.3(MYH11):c.2412-9C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00235 in 1,610,528 control chromosomes in the GnomAD database, including 71 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_002474.3 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 |
---|---|---|---|---|---|---|---|---|
MYH11 | NM_002474.3 | c.2412-9C>A | intron_variant | Intron 19 of 40 | ENST00000300036.6 | NP_002465.1 | ||
MYH11 | NM_001040113.2 | c.2433-9C>A | intron_variant | Intron 20 of 42 | ENST00000452625.7 | NP_001035202.1 | ||
MYH11 | NM_001040114.2 | c.2433-9C>A | intron_variant | Intron 20 of 41 | NP_001035203.1 | |||
MYH11 | NM_022844.3 | c.2412-9C>A | intron_variant | Intron 19 of 41 | NP_074035.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MYH11 | ENST00000300036.6 | c.2412-9C>A | intron_variant | Intron 19 of 40 | 1 | NM_002474.3 | ENSP00000300036.5 | |||
MYH11 | ENST00000452625.7 | c.2433-9C>A | intron_variant | Intron 20 of 42 | 1 | NM_001040113.2 | ENSP00000407821.2 |
Frequencies
GnomAD3 genomes AF: 0.0123 AC: 1872AN: 152070Hom.: 38 Cov.: 32
GnomAD3 exomes AF: 0.00337 AC: 844AN: 250446Hom.: 14 AF XY: 0.00246 AC XY: 333AN XY: 135412
GnomAD4 exome AF: 0.00131 AC: 1904AN: 1458338Hom.: 33 Cov.: 31 AF XY: 0.00108 AC XY: 781AN XY: 725652
GnomAD4 genome AF: 0.0123 AC: 1874AN: 152190Hom.: 38 Cov.: 32 AF XY: 0.0118 AC XY: 879AN XY: 74412
ClinVar
Submissions by phenotype
not specified Benign:4
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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. -
Familial thoracic aortic aneurysm and aortic dissection Benign:2
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Aortic aneurysm, familial thoracic 4 Benign:2
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This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
Familial aortopathy Benign:1
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not provided Benign:1
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Connective tissue disorder Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at