chr16-15717238-G-T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 1P and 4B. PP2BP4_Strong
The NM_002474.3(MYH11):c.5406C>A(p.His1802Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000103 in 1,461,846 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. H1802Y) has been classified as Uncertain significance.
Frequency
Consequence
NM_002474.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MYH11 | NM_002474.3 | c.5406C>A | p.His1802Gln | missense_variant | 38/41 | ENST00000300036.6 | |
MYH11 | NM_001040113.2 | c.5427C>A | p.His1809Gln | missense_variant | 39/43 | ENST00000452625.7 | |
NDE1 | NM_017668.3 | c.948-6953G>T | intron_variant | ENST00000396354.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MYH11 | ENST00000300036.6 | c.5406C>A | p.His1802Gln | missense_variant | 38/41 | 1 | NM_002474.3 | P3 | |
MYH11 | ENST00000452625.7 | c.5427C>A | p.His1809Gln | missense_variant | 39/43 | 1 | NM_001040113.2 | ||
NDE1 | ENST00000396354.6 | c.948-6953G>T | intron_variant | 1 | NM_017668.3 | P1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 0.0000103 AC: 15AN: 1461846Hom.: 0 Cov.: 33 AF XY: 0.00000963 AC XY: 7AN XY: 727234
GnomAD4 genome Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at