10-13175652-T-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_018518.5(MCM10):c.735T>G(p.Cys245Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000869 in 1,610,884 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_018518.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MCM10 | NM_018518.5 | c.735T>G | p.Cys245Trp | missense_variant | 6/20 | ENST00000378714.8 | |
MCM10 | NM_182751.3 | c.738T>G | p.Cys246Trp | missense_variant | 6/20 | ||
MCM10 | XM_011519538.3 | c.738T>G | p.Cys246Trp | missense_variant | 6/20 | ||
MCM10 | XM_047425437.1 | c.735T>G | p.Cys245Trp | missense_variant | 6/20 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MCM10 | ENST00000378714.8 | c.735T>G | p.Cys245Trp | missense_variant | 6/20 | 1 | NM_018518.5 | P4 | |
MCM10 | ENST00000484800.6 | c.738T>G | p.Cys246Trp | missense_variant | 6/20 | 1 | A1 | ||
MCM10 | ENST00000378694.1 | c.735T>G | p.Cys245Trp | missense_variant | 5/18 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000591 AC: 9AN: 152180Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 249354Hom.: 0 AF XY: 0.00000742 AC XY: 1AN XY: 134792
GnomAD4 exome AF: 0.00000343 AC: 5AN: 1458704Hom.: 0 Cov.: 30 AF XY: 0.00000138 AC XY: 1AN XY: 725440
GnomAD4 genome ? AF: 0.0000591 AC: 9AN: 152180Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74348
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 09, 2023 | The c.738T>G (p.C246W) alteration is located in exon 6 (coding exon 5) of the MCM10 gene. This alteration results from a T to G substitution at nucleotide position 738, causing the cysteine (C) at amino acid position 246 to be replaced by a tryptophan (W). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at