16-15708817-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBP6_Very_Strong
The NM_001040113.2(MYH11):c.5832G>A(p.Ser1944=) variant causes a synonymous change. The variant allele was found at a frequency of 0.0000292 in 1,608,956 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. S1944S) has been classified as Uncertain significance.
Frequency
Consequence
NM_001040113.2 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MYH11 | NM_001040113.2 | c.5832G>A | p.Ser1944= | synonymous_variant | 42/43 | ENST00000452625.7 | |
MYH11 | NM_002474.3 | c.5787-4694G>A | intron_variant | ENST00000300036.6 | |||
NDE1 | NM_017668.3 | c.947+11957C>T | intron_variant | ENST00000396354.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MYH11 | ENST00000452625.7 | c.5832G>A | p.Ser1944= | synonymous_variant | 42/43 | 1 | NM_001040113.2 | ||
MYH11 | ENST00000300036.6 | c.5787-4694G>A | intron_variant | 1 | NM_002474.3 | P3 | |||
NDE1 | ENST00000396354.6 | c.947+11957C>T | intron_variant | 1 | NM_017668.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152142Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000372 AC: 9AN: 241780Hom.: 0 AF XY: 0.0000153 AC XY: 2AN XY: 130362
GnomAD4 exome AF: 0.0000268 AC: 39AN: 1456814Hom.: 0 Cov.: 32 AF XY: 0.0000207 AC XY: 15AN XY: 724006
GnomAD4 genome AF: 0.0000526 AC: 8AN: 152142Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74322
ClinVar
Submissions by phenotype
Familial thoracic aortic aneurysm and aortic dissection Benign:2
Likely benign, criteria provided, single submitter | clinical testing | All of Us Research Program, National Institutes of Health | Feb 05, 2024 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Color Diagnostics, LLC DBA Color Health | May 13, 2019 | - - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Apr 14, 2024 | - - |
Aortic aneurysm, familial thoracic 4 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 16, 2024 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 22, 2020 | Has not been previously published as pathogenic or benign to our knowledge; In silico analysis supports that this variant does not alter splicing - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at