rs3087450
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_004526.4(MCM2):c.1186G>A(p.Ala396Thr) variant causes a missense change. The variant allele was found at a frequency of 0.0107 in 1,614,204 control chromosomes in the GnomAD database, including 121 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely 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 -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MCM2 | NM_004526.4 | c.1186G>A | p.Ala396Thr | missense_variant | 7/16 | ENST00000265056.12 | |
MCM2 | XM_024453531.2 | c.1159G>A | p.Ala387Thr | missense_variant | 7/16 | ||
MCM2 | NR_073375.2 | n.1261G>A | non_coding_transcript_exon_variant | 7/16 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MCM2 | ENST00000265056.12 | c.1186G>A | p.Ala396Thr | missense_variant | 7/16 | 1 | NM_004526.4 | P1 | |
MCM2 | ENST00000491422.1 | c.775G>A | p.Ala259Thr | missense_variant | 4/14 | 5 | |||
MCM2 | ENST00000474964.5 | c.*764G>A | 3_prime_UTR_variant, NMD_transcript_variant | 7/16 | 2 | ||||
MCM2 | ENST00000477668.5 | c.*764G>A | 3_prime_UTR_variant, NMD_transcript_variant | 6/14 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00832 AC: 1266AN: 152224Hom.: 15 Cov.: 32
GnomAD3 exomes AF: 0.00804 AC: 2020AN: 251380Hom.: 9 AF XY: 0.00829 AC XY: 1126AN XY: 135878
GnomAD4 exome AF: 0.0110 AC: 16025AN: 1461862Hom.: 106 Cov.: 31 AF XY: 0.0109 AC XY: 7931AN XY: 727230
GnomAD4 genome ? AF: 0.00831 AC: 1266AN: 152342Hom.: 15 Cov.: 32 AF XY: 0.00796 AC XY: 593AN XY: 74488
ClinVar
Submissions by phenotype
not provided Benign:3
Likely benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Aug 10, 2018 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 24, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Apr 01, 2023 | MCM2: BS1, BS2 - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jan 31, 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 | Sep 25, 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