rs771063151
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP6_Very_StrongBS1
The NM_001190787.3(MCIDAS):c.218-6_218-5insTCTCCCCG variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000724 in 1,499,124 control chromosomes in the GnomAD database, including 5 homozygotes. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.00049 ( 0 hom., cov: 33)
Exomes 𝑓: 0.00075 ( 5 hom. )
Consequence
MCIDAS
NM_001190787.3 splice_region, splice_polypyrimidine_tract, intron
NM_001190787.3 splice_region, splice_polypyrimidine_tract, intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -0.252
Genes affected
MCIDAS (HGNC:40050): (multiciliate differentiation and DNA synthesis associated cell cycle protein) This gene encodes a member of the geminin family of proteins. The encoded nuclear protein is required for the generation of multiciliated cells in respiratory epithelium. Mutations in this gene cause a rare mucociliary clearance disorder associated with recurring respiratory infections in human patients, known as reduced generation of multiple motile cilia (RGMC). [provided by RefSeq, Sep 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP6
?
Variant 5-55226672-G-GCGGGGAGA is Benign according to our data. Variant chr5-55226672-G-GCGGGGAGA is described in ClinVar as [Likely_benign]. Clinvar id is 454527.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS1
?
Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.000492 (75/152314) while in subpopulation SAS AF= 0.00145 (7/4830). AF 95% confidence interval is 0.000679. There are 0 homozygotes in gnomad4. There are 37 alleles in male gnomad4 subpopulation. This position pass quality control queck.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MCIDAS | NM_001190787.3 | c.218-6_218-5insTCTCCCCG | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000513312.3 | |||
LOC124900978 | XR_007058773.1 | n.57_64dup | non_coding_transcript_exon_variant | 1/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MCIDAS | ENST00000513312.3 | c.218-6_218-5insTCTCCCCG | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_001190787.3 | P1 | |||
MCIDAS | ENST00000513468.5 | c.218-6_218-5insTCTCCCCG | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, NMD_transcript_variant | 5 | |||||
MCIDAS | ENST00000515336.1 | n.155-6_155-5insTCTCCCCG | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.000493 AC: 75AN: 152196Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.000357 AC: 35AN: 97914Hom.: 0 AF XY: 0.000389 AC XY: 21AN XY: 53982
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GnomAD4 exome AF: 0.000750 AC: 1010AN: 1346810Hom.: 5 Cov.: 31 AF XY: 0.000775 AC XY: 513AN XY: 662288
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ClinVar
Significance: Likely benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Primary ciliary dyskinesia Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Oct 17, 2023 | - - |
MCIDAS-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | May 19, 2022 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Ciliary dyskinesia, primary, 42 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Feb 24, 2022 | - - |
Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at