rs73598041
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The ENST00000375940.9(MASTL):c.2483-33T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0478 in 1,592,828 control chromosomes in the GnomAD database, including 2,009 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.056 ( 257 hom., cov: 33)
Exomes 𝑓: 0.047 ( 1752 hom. )
Consequence
MASTL
ENST00000375940.9 intron
ENST00000375940.9 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.14
Genes affected
MASTL (HGNC:19042): (microtubule associated serine/threonine kinase like) This gene encodes a microtubule-associated serine/threonine kinase. Mutations at this locus have been associated with autosomal dominant thrombocytopenia, also known as thrombocytopenia-2. Alternatively spliced transcript variants have been described for this locus. [provided by RefSeq, Feb 2010]
ACBD5 (HGNC:23338): (acyl-CoA binding domain containing 5) This gene encodes a member of the acyl-Coenzyme A binding protein family, known to function in the transport and distribution of long chain acyl-Coenzyme A in cells. This gene may play a role in the differentiation of megakaryocytes and formation of platelets. A related protein in yeast is involved in autophagy of peroxisomes. A mutation in this gene has been associated with autosomal dominant thrombocytopenia. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2014]
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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=-0.84).
BP6
Variant 10-27186346-T-C is Benign according to our data. Variant chr10-27186346-T-C is described in ClinVar as [Benign]. Clinvar id is 262121.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0802 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MASTL | NM_001172303.3 | c.2483-33T>C | intron_variant | ENST00000375940.9 | NP_001165774.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MASTL | ENST00000375940.9 | c.2483-33T>C | intron_variant | 1 | NM_001172303.3 | ENSP00000365107 | P5 |
Frequencies
GnomAD3 genomes AF: 0.0558 AC: 8490AN: 152180Hom.: 255 Cov.: 33
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GnomAD3 exomes AF: 0.0439 AC: 11018AN: 250982Hom.: 310 AF XY: 0.0435 AC XY: 5906AN XY: 135736
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GnomAD4 exome AF: 0.0470 AC: 67675AN: 1440530Hom.: 1752 Cov.: 28 AF XY: 0.0467 AC XY: 33539AN XY: 718024
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GnomAD4 genome AF: 0.0559 AC: 8511AN: 152298Hom.: 257 Cov.: 33 AF XY: 0.0547 AC XY: 4076AN XY: 74474
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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:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 19, 2021 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at