chr20-5954679-T-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_032485.6(MCM8):c.325T>G(p.Leu109Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000709 in 1,591,548 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0040 ( 3 hom., cov: 32)
Exomes 𝑓: 0.00036 ( 2 hom. )
Consequence
MCM8
NM_032485.6 missense
NM_032485.6 missense
Scores
4
13
Clinical Significance
Conservation
PhyloP100: 1.13
Genes affected
MCM8 (HGNC:16147): (minichromosome maintenance 8 homologous recombination repair factor) The protein encoded by this gene is one of the highly conserved mini-chromosome maintenance proteins (MCM) that are essential for the initiation of eukaryotic genome replication. The hexameric protein complex formed by the mini-chromosome maintenance proteins is a key component of the pre-replication complex and may be involved in the formation of replication forks and in the recruitment of other DNA replication related proteins. This protein contains the central domain that is conserved among the mini-chromosome maintenance proteins. The encoded protein may interact with other mini-chromosome maintenance proteins and play a role in DNA replication. This gene may be associated with length of reproductive lifespan and menopause. Alternatively spliced transcript variants encoding distinct isoforms have been described. [provided by RefSeq, Jul 2013]
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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 (MetaRNN=0.0052725375).
BP6
?
Variant 20-5954679-T-G is Benign according to our data. Variant chr20-5954679-T-G is described in ClinVar as [Benign]. Clinvar id is 790768.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.004 (609/152346) while in subpopulation AFR AF= 0.0138 (575/41580). AF 95% confidence interval is 0.0129. There are 3 homozygotes in gnomad4. There are 294 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 3 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MCM8 | NM_032485.6 | c.325T>G | p.Leu109Val | missense_variant | 4/19 | ENST00000610722.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MCM8 | ENST00000610722.4 | c.325T>G | p.Leu109Val | missense_variant | 4/19 | 1 | NM_032485.6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00399 AC: 607AN: 152228Hom.: 3 Cov.: 32
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GnomAD3 exomes AF: 0.00102 AC: 256AN: 250634Hom.: 1 AF XY: 0.000863 AC XY: 117AN XY: 135530
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GnomAD4 exome AF: 0.000361 AC: 519AN: 1439202Hom.: 2 Cov.: 26 AF XY: 0.000315 AC XY: 226AN XY: 717312
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GnomAD4 genome ? AF: 0.00400 AC: 609AN: 152346Hom.: 3 Cov.: 32 AF XY: 0.00395 AC XY: 294AN XY: 74500
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | May 04, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Uncertain
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;D;D;.;D
MetaRNN
Benign
T;T;T;T;T
MetaSVM
Benign
T
MutationAssessor
Uncertain
M;M;M;M;M
MutationTaster
Benign
D;D;D;D
PrimateAI
Benign
T
PROVEAN
Benign
N;N;N;.;N
REVEL
Benign
Sift
Benign
T;T;T;.;T
Sift4G
Benign
T;T;T;T;T
Polyphen
B;B;.;B;B
Vest4
MVP
MPC
0.24
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
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