chr17-12717394-G-A
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_001146312.3(MYOCD):c.226G>A(p.Asp76Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000784 in 1,613,906 control chromosomes in the GnomAD database, including 8 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0036 ( 6 hom., cov: 31)
Exomes 𝑓: 0.00049 ( 2 hom. )
Consequence
MYOCD
NM_001146312.3 missense
NM_001146312.3 missense
Scores
17
Clinical Significance
Conservation
PhyloP100: 1.85
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 -10 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.005953878).
BP6
Variant 17-12717394-G-A is Benign according to our data. Variant chr17-12717394-G-A is described in ClinVar as [Benign]. Clinvar id is 768833.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High AC in GnomAd4 at 552 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MYOCD | NM_001146312.3 | c.226G>A | p.Asp76Asn | missense_variant | 4/14 | ENST00000425538.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MYOCD | ENST00000425538.6 | c.226G>A | p.Asp76Asn | missense_variant | 4/14 | 1 | NM_001146312.3 | P2 | |
MYOCD | ENST00000343344.8 | c.226G>A | p.Asp76Asn | missense_variant | 4/13 | 1 | A2 | ||
MYOCD | ENST00000579237.5 | downstream_gene_variant | 4 |
Frequencies
GnomAD3 genomes AF: 0.00363 AC: 552AN: 152138Hom.: 6 Cov.: 31
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GnomAD3 exomes AF: 0.00118 AC: 296AN: 251122Hom.: 0 AF XY: 0.000847 AC XY: 115AN XY: 135700
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GnomAD4 exome AF: 0.000488 AC: 714AN: 1461650Hom.: 2 Cov.: 30 AF XY: 0.000433 AC XY: 315AN XY: 727110
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GnomAD4 genome AF: 0.00363 AC: 552AN: 152256Hom.: 6 Cov.: 31 AF XY: 0.00344 AC XY: 256AN XY: 74442
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | May 08, 2017 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
D
LIST_S2
Benign
T;T
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationAssessor
Benign
N;N
MutationTaster
Benign
N;N
PrimateAI
Benign
T
PROVEAN
Benign
N;N
REVEL
Benign
Sift
Benign
T;T
Sift4G
Benign
T;T
Polyphen
B;B
Vest4
MVP
MPC
ClinPred
T
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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