17-12763317-C-T
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Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_001146312.3(MYOCD):c.2634C>T(p.Ser878Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00353 in 1,608,058 control chromosomes in the GnomAD database, including 170 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.017 ( 94 hom., cov: 32)
Exomes 𝑓: 0.0021 ( 76 hom. )
Consequence
MYOCD
NM_001146312.3 synonymous
NM_001146312.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.76
Genes affected
MYOCD (HGNC:16067): (myocardin) This gene encodes a nuclear protein, which is expressed in heart, aorta, and in smooth muscle cell-containing tissues. It functions as a transcriptional co-activator of serum response factor (SRF) and modulates expression of cardiac and smooth muscle-specific SRF-target genes, and thus may play a crucial role in cardiogenesis and differentiation of the smooth muscle cell lineage. Alternatively spliced transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Sep 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -21 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BP6
Variant 17-12763317-C-T is Benign according to our data. Variant chr17-12763317-C-T is described in ClinVar as [Benign]. Clinvar id is 780416.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=-2.76 with no splicing effect.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0557 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MYOCD | NM_001146312.3 | c.2634C>T | p.Ser878Ser | synonymous_variant | 14/14 | ENST00000425538.6 | NP_001139784.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MYOCD | ENST00000425538.6 | c.2634C>T | p.Ser878Ser | synonymous_variant | 14/14 | 1 | NM_001146312.3 | ENSP00000401678.1 | ||
MYOCD | ENST00000343344.8 | c.2490C>T | p.Ser830Ser | synonymous_variant | 13/13 | 1 | ENSP00000341835.4 | |||
MYOCD | ENST00000443061.1 | c.1620C>T | p.Ser540Ser | synonymous_variant | 6/6 | 1 | ENSP00000400148.2 | |||
ARHGAP44-AS1 | ENST00000584772.1 | n.502G>A | non_coding_transcript_exon_variant | 2/2 | 1 |
Frequencies
GnomAD3 genomes AF: 0.0170 AC: 2578AN: 152030Hom.: 92 Cov.: 32
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GnomAD3 exomes AF: 0.00499 AC: 1225AN: 245680Hom.: 39 AF XY: 0.00368 AC XY: 488AN XY: 132752
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GnomAD4 exome AF: 0.00212 AC: 3092AN: 1455910Hom.: 76 Cov.: 31 AF XY: 0.00188 AC XY: 1358AN XY: 724022
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GnomAD4 genome AF: 0.0170 AC: 2590AN: 152148Hom.: 94 Cov.: 32 AF XY: 0.0169 AC XY: 1257AN XY: 74390
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ClinVar
Significance: Benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:3
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 31, 2019 | - - |
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 09, 2021 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
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