chr3-127599515-T-G
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_004526.4(MCM2):c.204T>G(p.Asp68Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0024 in 1,613,972 control chromosomes in the GnomAD database, including 68 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_004526.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MCM2 | NM_004526.4 | c.204T>G | p.Asp68Glu | missense_variant | 2/16 | ENST00000265056.12 | |
MCM2 | XM_024453531.2 | c.177T>G | p.Asp59Glu | missense_variant | 2/16 | ||
MCM2 | NR_073375.2 | n.260T>G | non_coding_transcript_exon_variant | 2/16 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MCM2 | ENST00000265056.12 | c.204T>G | p.Asp68Glu | missense_variant | 2/16 | 1 | NM_004526.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0126 AC: 1914AN: 152130Hom.: 35 Cov.: 33
GnomAD3 exomes AF: 0.00328 AC: 824AN: 251094Hom.: 15 AF XY: 0.00227 AC XY: 308AN XY: 135736
GnomAD4 exome AF: 0.00134 AC: 1958AN: 1461724Hom.: 33 Cov.: 30 AF XY: 0.00113 AC XY: 825AN XY: 727154
GnomAD4 genome ? AF: 0.0126 AC: 1915AN: 152248Hom.: 35 Cov.: 33 AF XY: 0.0117 AC XY: 874AN XY: 74442
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 15, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 04, 2018 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
MCM2-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jul 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). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at