5-55220668-C-T
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 2P and 16B. PM2BP4_StrongBP6_Very_StrongBS1
The NM_001190787.3(MCIDAS):c.856G>A(p.Glu286Lys) variant causes a missense change. The variant allele was found at a frequency of 0.000411 in 1,536,098 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.0022 ( 0 hom., cov: 33)
Exomes 𝑓: 0.00021 ( 0 hom. )
Consequence
MCIDAS
NM_001190787.3 missense
NM_001190787.3 missense
Scores
6
12
Clinical Significance
Conservation
PhyloP100: 4.69
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 -14 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.00573346).
BP6
Variant 5-55220668-C-T is Benign according to our data. Variant chr5-55220668-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 238623.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00221 (337/152342) while in subpopulation AFR AF= 0.00777 (323/41582). AF 95% confidence interval is 0.00707. There are 0 homozygotes in gnomad4. There are 165 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MCIDAS | ENST00000513312.3 | c.856G>A | p.Glu286Lys | missense_variant | 7/7 | 1 | NM_001190787.3 | ENSP00000426359.1 | ||
MCIDAS | ENST00000513468.5 | n.*320G>A | non_coding_transcript_exon_variant | 7/7 | 5 | ENSP00000422165.1 | ||||
MCIDAS | ENST00000513468.5 | n.*320G>A | 3_prime_UTR_variant | 7/7 | 5 | ENSP00000422165.1 |
Frequencies
GnomAD3 genomes AF: 0.00221 AC: 337AN: 152224Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.000490 AC: 66AN: 134582Hom.: 0 AF XY: 0.000368 AC XY: 27AN XY: 73304
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GnomAD4 exome AF: 0.000212 AC: 294AN: 1383756Hom.: 0 Cov.: 30 AF XY: 0.000170 AC XY: 116AN XY: 682822
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GnomAD4 genome AF: 0.00221 AC: 337AN: 152342Hom.: 0 Cov.: 33 AF XY: 0.00221 AC XY: 165AN XY: 74492
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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 | Labcorp Genetics (formerly Invitae), Labcorp | Jan 13, 2025 | - - |
MCIDAS-related disorder Benign:1
Benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Sep 12, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
not provided Benign:1
Likely benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Benign
T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Benign
L
PrimateAI
Uncertain
T
PROVEAN
Benign
N
REVEL
Benign
Sift
Uncertain
D
Sift4G
Benign
T
Polyphen
P
Vest4
MVP
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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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