chr6-24777238-A-G
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_015895.5(GMNN):c.-9A>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000127 in 1,351,632 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.00038 ( 1 hom., cov: 32)
Exomes 𝑓: 0.000095 ( 0 hom. )
Consequence
GMNN
NM_015895.5 5_prime_UTR
NM_015895.5 5_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.33
Genes affected
GMNN (HGNC:17493): (geminin DNA replication inhibitor) This gene encodes a protein that plays a critical role in cell cycle regulation. The encoded protein inhibits DNA replication by binding to DNA replication factor Cdt1, preventing the incorporation of minichromosome maintenance proteins into the pre-replication complex. The encoded protein is expressed during the S and G2 phases of the cell cycle and is degraded by the anaphase-promoting complex during the metaphase-anaphase transition. Increased expression of this gene may play a role in several malignancies including colon, rectal and breast cancer. Alternatively spliced transcript variants have been observed for this gene, and two pseudogenes of this gene are located on the short arm of chromosome 16. [provided by RefSeq, Oct 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.8).
BP6
?
Variant 6-24777238-A-G is Benign according to our data. Variant chr6-24777238-A-G is described in ClinVar as [Benign]. Clinvar id is 3049761.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High AC in GnomAd at 59 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GMNN | NM_015895.5 | c.-9A>G | 5_prime_UTR_variant | 2/7 | ENST00000230056.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GMNN | ENST00000230056.8 | c.-9A>G | 5_prime_UTR_variant | 2/7 | 1 | NM_015895.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000388 AC: 59AN: 152216Hom.: 1 Cov.: 32
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GnomAD3 exomes AF: 0.000554 AC: 110AN: 198536Hom.: 0 AF XY: 0.000578 AC XY: 63AN XY: 108942
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GnomAD4 exome AF: 0.0000951 AC: 114AN: 1199298Hom.: 0 Cov.: 16 AF XY: 0.0000924 AC XY: 56AN XY: 606072
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GnomAD4 genome ? AF: 0.000381 AC: 58AN: 152334Hom.: 1 Cov.: 32 AF XY: 0.000510 AC XY: 38AN XY: 74488
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
GMNN-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jul 23, 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
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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