rs759520932
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 1P and 4B. PP2BS2
The NM_002471.4(MYH6):c.1244G>C(p.Gly415Ala) variant causes a missense change. The variant allele was found at a frequency of 0.0000421 in 1,614,106 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G415R) has been classified as Likely benign.
Frequency
Consequence
NM_002471.4 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 |
---|---|---|---|---|---|---|---|
MYH6 | NM_002471.4 | c.1244G>C | p.Gly415Ala | missense_variant | 13/39 | ENST00000405093.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MYH6 | ENST00000405093.9 | c.1244G>C | p.Gly415Ala | missense_variant | 13/39 | 5 | NM_002471.4 | P1 | |
MYH6 | ENST00000557461.2 | n.1311G>C | non_coding_transcript_exon_variant | 13/14 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000657 AC: 10AN: 152212Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000107 AC: 27AN: 251482Hom.: 0 AF XY: 0.000103 AC XY: 14AN XY: 135922
GnomAD4 exome AF: 0.0000397 AC: 58AN: 1461894Hom.: 0 Cov.: 32 AF XY: 0.0000426 AC XY: 31AN XY: 727248
GnomAD4 genome ? AF: 0.0000657 AC: 10AN: 152212Hom.: 0 Cov.: 32 AF XY: 0.0000941 AC XY: 7AN XY: 74360
ClinVar
Submissions by phenotype
Dilated cardiomyopathy 1EE;C2750467:Hypertrophic cardiomyopathy 14;C3279790:Atrial septal defect 3;C3279791:Sick sinus syndrome 3, susceptibility to;C3495498:Hypertrophic cardiomyopathy 1 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Oct 31, 2018 | - - |
Dilated cardiomyopathy 1EE;C2750467:Hypertrophic cardiomyopathy 14;C3279791:Sick sinus syndrome 3, susceptibility to Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | New York Genome Center | Jan 19, 2023 | The c.1244G>C p.(Gly415Ala) variant identified in the MYH6 gene substitutes a conserved Glycine for Alanine at amino acid 415/1940 (exon 13/39). This variant is found with low frequency in population databases (gnomADv2.1.1, gnomADv3.1.2, BRAVO-TOPMed) with allele frequency 1.09e-4 suggesting it is not a common benign variant in the populations represented in those databases. In silico algorithms predict this variant to be damaging to the function of the canonical transcript (REVEL=0.803). The c.1244G>C p.(Gly415Ala) variant is reported in ClinVar (VarID:239163) as both a Variant of Uncertain Significance (n=2) and as Likely Benign (n=1), however the evidence used for the Likely Benign assertion was not available for our review. This variant was identified in a single patient who underwent genetic testing with a cardiomyopathy gene panel, however detailed clinical information was not available for that individual and the c.1244G>C p.(Gly415Ala) variant was considered of uncertain clinical significance ([PMID:30847666] Supp File 2). Given the lack of compelling evidence for its pathogenicity, the c.1244G>C p.(Gly415Ala) variant identified in the MYH6 gene is reported as a Variant of Uncertain Significance. - |
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Feb 07, 2023 | - - |
Cardiovascular phenotype Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 26, 2022 | The p.G415A variant (also known as c.1244G>C), located in coding exon 11 of the MYH6 gene, results from a G to C substitution at nucleotide position 1244. The glycine at codon 415 is replaced by alanine, an amino acid with similar properties. This variant was detected in a cardiomyopathy genetic testing cohort; however, clinical details were limited (van Lint FHM et al. Neth Heart J, 2019 Jun;27:304-309). This amino acid position is highly conserved in available vertebrate species. In addition, the in silico prediction for this alteration is inconclusive. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. - |
Hypertrophic cardiomyopathy 14 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Aug 28, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at