chr10-13170884-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_018518.5(MCM10):c.8-38C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.79 in 1,558,772 control chromosomes in the GnomAD database, including 490,402 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.77 ( 44981 hom., cov: 33)
Exomes 𝑓: 0.79 ( 445421 hom. )
Consequence
MCM10
NM_018518.5 intron
NM_018518.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.68
Genes affected
MCM10 (HGNC:18043): (minichromosome maintenance 10 replication initiation factor) The protein encoded by this gene is one of the highly conserved mini-chromosome maintenance proteins (MCM) that are involved in the initiation of eukaryotic genome replication. The hexameric protein complex formed by MCM proteins is a key component of the pre-replication complex (pre-RC) and it may be involved in the formation of replication forks and in the recruitment of other DNA replication related proteins. This protein can interact with MCM2 and MCM6, as well as with the origin recognition protein ORC2. It is regulated by proteolysis and phosphorylation in a cell cycle-dependent manner. Studies of a similar protein in Xenopus suggest that the chromatin binding of this protein at the onset of DNA replication is after pre-RC assembly and before origin unwinding. Alternatively spliced transcript variants encoding distinct isoforms have been identified. [provided by RefSeq, Jul 2008]
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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=-0.97).
BP6
?
Variant 10-13170884-C-T is Benign according to our data. Variant chr10-13170884-C-T is described in ClinVar as [Benign]. Clinvar id is 2687950.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.801 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MCM10 | NM_018518.5 | c.8-38C>T | intron_variant | ENST00000378714.8 | |||
MCM10 | NM_182751.3 | c.8-38C>T | intron_variant | ||||
MCM10 | XM_011519538.3 | c.8-38C>T | intron_variant | ||||
MCM10 | XM_047425437.1 | c.8-38C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MCM10 | ENST00000378714.8 | c.8-38C>T | intron_variant | 1 | NM_018518.5 | P4 | |||
MCM10 | ENST00000484800.6 | c.8-38C>T | intron_variant | 1 | A1 | ||||
MCM10 | ENST00000378694.1 | c.8-38C>T | intron_variant | 5 | |||||
MCM10 | ENST00000479669.5 | c.-233-38C>T | intron_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.765 AC: 116311AN: 152034Hom.: 44941 Cov.: 33
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GnomAD3 exomes AF: 0.729 AC: 169652AN: 232844Hom.: 63642 AF XY: 0.738 AC XY: 93547AN XY: 126824
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GnomAD4 exome AF: 0.792 AC: 1114383AN: 1406620Hom.: 445421 Cov.: 22 AF XY: 0.791 AC XY: 553379AN XY: 699580
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GnomAD4 genome ? AF: 0.765 AC: 116398AN: 152152Hom.: 44981 Cov.: 33 AF XY: 0.758 AC XY: 56358AN XY: 74372
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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 | Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan | Jan 24, 2024 | This variant is classified as Benign based on local population frequency. This variant was detected in 88% of patients studied by a panel of primary immunodeficiencies. Number of patients: 84. Only high quality variants are reported. - |
Computational scores
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BayesDel_noAF
Benign
Cadd
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Dann
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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