chr17-12744173-T-C
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001146312.3(MYOCD):c.718-10T>C variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.833 in 1,612,934 control chromosomes in the GnomAD database, including 562,590 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.81 ( 49894 hom., cov: 32)
Exomes 𝑓: 0.84 ( 512696 hom. )
Consequence
MYOCD
NM_001146312.3 splice_polypyrimidine_tract, intron
NM_001146312.3 splice_polypyrimidine_tract, intron
Scores
2
Splicing: ADA: 0.0001284
2
Clinical Significance
Conservation
PhyloP100: 0.102
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 -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BP6
Variant 17-12744173-T-C is Benign according to our data. Variant chr17-12744173-T-C is described in ClinVar as [Benign]. Clinvar id is 1181987.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.853 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MYOCD | NM_001146312.3 | c.718-10T>C | splice_polypyrimidine_tract_variant, intron_variant | ENST00000425538.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MYOCD | ENST00000425538.6 | c.718-10T>C | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_001146312.3 | P2 | |||
MYOCD | ENST00000343344.8 | c.718-10T>C | splice_polypyrimidine_tract_variant, intron_variant | 1 | A2 | ||||
MYOCD | ENST00000395988.1 | n.638-10T>C | splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.808 AC: 122798AN: 152064Hom.: 49859 Cov.: 32
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GnomAD3 exomes AF: 0.805 AC: 199852AN: 248364Hom.: 81140 AF XY: 0.808 AC XY: 108644AN XY: 134466
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GnomAD4 exome AF: 0.836 AC: 1221134AN: 1460752Hom.: 512696 Cov.: 52 AF XY: 0.833 AC XY: 605580AN XY: 726632
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GnomAD4 genome AF: 0.807 AC: 122883AN: 152182Hom.: 49894 Cov.: 32 AF XY: 0.805 AC XY: 59923AN XY: 74422
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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 | GeneDx | Nov 12, 2018 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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dbscSNV1_ADA
Benign
dbscSNV1_RF
Benign
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at