rs3729810
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The ENST00000355349.4(MYH7):c.999+44T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0961 in 1,508,828 control chromosomes in the GnomAD database, including 11,449 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.17 ( 4003 hom., cov: 32)
Exomes 𝑓: 0.087 ( 7446 hom. )
Consequence
MYH7
ENST00000355349.4 intron
ENST00000355349.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.265
Genes affected
MYH7 (HGNC:7577): (myosin heavy chain 7) Muscle myosin is a hexameric protein containing 2 heavy chain subunits, 2 alkali light chain subunits, and 2 regulatory light chain subunits. This gene encodes the beta (or slow) heavy chain subunit of cardiac myosin. It is expressed predominantly in normal human ventricle. It is also expressed in skeletal muscle tissues rich in slow-twitch type I muscle fibers. Changes in the relative abundance of this protein and the alpha (or fast) heavy subunit of cardiac myosin correlate with the contractile velocity of cardiac muscle. Its expression is also altered during thyroid hormone depletion and hemodynamic overloading. Mutations in this gene are associated with familial hypertrophic cardiomyopathy, myosin storage myopathy, dilated cardiomyopathy, and Laing distal myopathy. [provided by RefSeq, May 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BP6
Variant 14-23430516-A-G is Benign according to our data. Variant chr14-23430516-A-G is described in ClinVar as [Benign]. Clinvar id is 255636.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr14-23430516-A-G is described in Lovd as [Benign].
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.413 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MYH7 | NM_000257.4 | c.999+44T>C | intron_variant | ENST00000355349.4 | NP_000248.2 | |||
MYH7 | NM_001407004.1 | c.999+44T>C | intron_variant | NP_001393933.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MYH7 | ENST00000355349.4 | c.999+44T>C | intron_variant | 1 | NM_000257.4 | ENSP00000347507 | P1 |
Frequencies
GnomAD3 genomes AF: 0.172 AC: 26175AN: 151774Hom.: 3989 Cov.: 32
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GnomAD3 exomes AF: 0.0951 AC: 22185AN: 233304Hom.: 1991 AF XY: 0.0908 AC XY: 11406AN XY: 125626
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GnomAD4 exome AF: 0.0875 AC: 118718AN: 1356936Hom.: 7446 Cov.: 22 AF XY: 0.0866 AC XY: 58831AN XY: 679258
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GnomAD4 genome AF: 0.173 AC: 26233AN: 151892Hom.: 4003 Cov.: 32 AF XY: 0.166 AC XY: 12290AN XY: 74242
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
not provided Benign:1
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
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DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at