rs1553255366
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP6_Moderate
The ENST00000366684.7(ACTA1):c.809-35_809-14delinsAGCTTCTGCTCACGCTCCCCCC variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: not found (cov: 31)
Consequence
ACTA1
ENST00000366684.7 splice_polypyrimidine_tract, intron
ENST00000366684.7 splice_polypyrimidine_tract, intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.611
Genes affected
ACTA1 (HGNC:129): (actin alpha 1, skeletal muscle) The product encoded by this gene belongs to the actin family of proteins, which are highly conserved proteins that play a role in cell motility, structure and integrity. Alpha, beta and gamma actin isoforms have been identified, with alpha actins being a major constituent of the contractile apparatus, while beta and gamma actins are involved in the regulation of cell motility. This actin is an alpha actin that is found in skeletal muscle. Mutations in this gene cause a variety of myopathies, including nemaline myopathy, congenital myopathy with excess of thin myofilaments, congenital myopathy with cores, and congenital myopathy with fiber-type disproportion, diseases that lead to muscle fiber defects with manifestations such as hypotonia. [provided by RefSeq, Sep 2019]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP6
Variant 1-229431916-CGGGGAGCGTGAGCAGAAGCTC-GGGGGGAGCGTGAGCAGAAGCT is Benign according to our data. Variant chr1-229431916-CGGGGAGCGTGAGCAGAAGCTC-GGGGGGAGCGTGAGCAGAAGCT is described in ClinVar as [Benign]. Clinvar id is 517171.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ACTA1 | NM_001100.4 | c.809-35_809-14delinsAGCTTCTGCTCACGCTCCCCCC | splice_polypyrimidine_tract_variant, intron_variant | ENST00000366684.7 | NP_001091.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ACTA1 | ENST00000366684.7 | c.809-35_809-14delinsAGCTTCTGCTCACGCTCCCCCC | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_001100.4 | ENSP00000355645 | P1 | |||
ACTA1 | ENST00000366683.4 | c.809-35_809-14delinsAGCTTCTGCTCACGCTCCCCCC | splice_polypyrimidine_tract_variant, intron_variant | 5 | ENSP00000355644 | |||||
ACTA1 | ENST00000684723.1 | c.674-35_674-14delinsAGCTTCTGCTCACGCTCCCCCC | splice_polypyrimidine_tract_variant, intron_variant | ENSP00000508084 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD3 genomes
Cov.:
31
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome Cov.: 31
GnomAD4 genome
Cov.:
31
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Dec 13, 2016 | c.809-35_809-14delins22 in intron 5 of ACTA1: This variant is not expected to ha ve clinical significance because it has been identified (as separate changes) in 15 - 21% of chromosomes from multiple diverse populations by the Genome Aggrega tion Database (gnomAD, http://gnomad.broadinstitute.org/; dbSNP: rs59228224; rs2 01427429; rs398123565) - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at