17-12760379-G-A
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001146312.3(MYOCD):c.2332-271G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.364 in 420,866 control chromosomes in the GnomAD database, including 31,148 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.31 ( 9047 hom., cov: 33)
Exomes 𝑓: 0.39 ( 22101 hom. )
Consequence
MYOCD
NM_001146312.3 intron
NM_001146312.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.402
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 -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BP6
Variant 17-12760379-G-A is Benign according to our data. Variant chr17-12760379-G-A is described in ClinVar as [Benign]. Clinvar id is 1272626.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.553 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MYOCD | NM_001146312.3 | c.2332-271G>A | intron_variant | ENST00000425538.6 | |||
ARHGAP44-AS1 | NR_104607.1 | n.3482C>T | non_coding_transcript_exon_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MYOCD | ENST00000425538.6 | c.2332-271G>A | intron_variant | 1 | NM_001146312.3 | P2 | |||
MYOCD | ENST00000343344.8 | c.2188-271G>A | intron_variant | 1 | A2 | ||||
MYOCD | ENST00000443061.1 | c.1318-271G>A | intron_variant | 1 | |||||
ARHGAP44-AS1 | ENST00000584772.1 | n.3440C>T | non_coding_transcript_exon_variant | 2/2 | 1 |
Frequencies
GnomAD3 genomes AF: 0.312 AC: 47512AN: 152048Hom.: 9046 Cov.: 33
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GnomAD4 exome AF: 0.394 AC: 105738AN: 268700Hom.: 22101 Cov.: 0 AF XY: 0.396 AC XY: 56077AN XY: 141468
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GnomAD4 genome AF: 0.312 AC: 47510AN: 152166Hom.: 9047 Cov.: 33 AF XY: 0.318 AC XY: 23674AN XY: 74386
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 12, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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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