chr2-151282008-T-C
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The NM_004688.3(NMI):āc.117A>Gā(p.Gln39=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.575 in 1,530,844 control chromosomes in the GnomAD database, including 256,080 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: š 0.60 ( 27219 hom., cov: 32)
Exomes š: 0.57 ( 228861 hom. )
Consequence
NMI
NM_004688.3 synonymous
NM_004688.3 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.69
Genes affected
NMI (HGNC:7854): (N-myc and STAT interactor) NMYC interactor (NMI) encodes a protein that interacts with NMYC and CMYC (two members of the oncogene Myc family), and other transcription factors containing a Zip, HLH, or HLH-Zip motif. The NMI protein also interacts with all STATs except STAT2 and augments STAT-mediated transcription in response to cytokines IL2 and IFN-gamma. The NMI mRNA has low expression levels in all human fetal and adult tissues tested except brain and has high expression in cancer cell line-myeloid leukemias. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.94).
BP7
Synonymous conserved (PhyloP=-1.69 with no splicing effect.
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.653 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NMI | NM_004688.3 | c.117A>G | p.Gln39= | synonymous_variant | 3/8 | ENST00000243346.10 | NP_004679.2 | |
NMI | XM_047446270.1 | c.390A>G | p.Gln130= | synonymous_variant | 3/8 | XP_047302226.1 | ||
NMI | XM_005246941.3 | c.117A>G | p.Gln39= | synonymous_variant | 3/8 | XP_005246998.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NMI | ENST00000243346.10 | c.117A>G | p.Gln39= | synonymous_variant | 3/8 | 1 | NM_004688.3 | ENSP00000243346 | P1 | |
NMI | ENST00000491771.5 | n.358+860A>G | intron_variant, non_coding_transcript_variant | 2 | ||||||
NMI | ENST00000414946.1 | downstream_gene_variant | 5 | ENSP00000387373 |
Frequencies
GnomAD3 genomes AF: 0.596 AC: 90442AN: 151872Hom.: 27189 Cov.: 32
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GnomAD3 exomes AF: 0.572 AC: 140373AN: 245298Hom.: 41007 AF XY: 0.563 AC XY: 74638AN XY: 132514
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GnomAD4 exome AF: 0.573 AC: 789724AN: 1378854Hom.: 228861 Cov.: 23 AF XY: 0.570 AC XY: 393136AN XY: 690222
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GnomAD4 genome AF: 0.596 AC: 90511AN: 151990Hom.: 27219 Cov.: 32 AF XY: 0.596 AC XY: 44269AN XY: 74274
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Not reported inComputational scores
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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