rs144571463
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 1P and 16B. PP2BP4_StrongBP6_Very_StrongBS2
The NM_002471.4(MYH6):c.5410C>A(p.Gln1804Lys) variant causes a missense change. The variant allele was found at a frequency of 0.000164 in 1,613,812 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. Q1804E) has been classified as Uncertain significance.
Frequency
Consequence
NM_002471.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -15 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MYH6 | NM_002471.4 | c.5410C>A | p.Gln1804Lys | missense_variant | 36/39 | ENST00000405093.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MYH6 | ENST00000405093.9 | c.5410C>A | p.Gln1804Lys | missense_variant | 36/39 | 5 | NM_002471.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000460 AC: 70AN: 152262Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.000358 AC: 90AN: 251476Hom.: 1 AF XY: 0.000346 AC XY: 47AN XY: 135916
GnomAD4 exome AF: 0.000134 AC: 196AN: 1461432Hom.: 2 Cov.: 34 AF XY: 0.000157 AC XY: 114AN XY: 727032
GnomAD4 genome AF: 0.000453 AC: 69AN: 152380Hom.: 1 Cov.: 33 AF XY: 0.000443 AC XY: 33AN XY: 74524
ClinVar
Submissions by phenotype
not specified Uncertain:1Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Mar 05, 2022 | - - |
Uncertain significance, flagged submission | clinical testing | GeneDx | Nov 30, 2016 | A variant of uncertain significance has been identified in the MYH6 gene. The Q1804K variant has been previously reported in one individual with HCM (Lopes et al., 2015); however, further clinical information and segregation data were not available. This substitution occurs at a position where amino acids with similar properties to Glutamine are tolerated across species, and Q1804K is a semi-conservative amino acid substitution, which may impact secondary protein structure as these residues differ in some properties. Nevertheless, in silico analysis is inconsistent in its predictions as to whether or not the variant is damaging to the protein structure/function. Furthermore, Q1804K was observed in approximately 0.11% of alleles from individuals of African ancestry in the NHLBI Exome Sequencing Project, and approximately 0.28-0.69% of alleles from individuals of East Asian ancestry, including one homozygous individual, in the 1000 Genomes Project and Exome Aggregation Consortium, indicating it may be a rare benign variant in these populations. Therefore, based on the currently available information, it is unclear whether this variant is pathogenic or rare benign. - |
Hypertrophic cardiomyopathy 14 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 14, 2024 | - - |
Cardiomyopathy Benign:1
Benign, criteria provided, single submitter | clinical testing | CHEO Genetics Diagnostic Laboratory, Children's Hospital of Eastern Ontario | Aug 23, 2019 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 04, 2021 | This variant is associated with the following publications: (PMID: 23396983, 27082122, 25351510) - |
MYH6-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Aug 13, 2020 | 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). - |
Cardiovascular phenotype Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 17, 2019 | 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. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at