chr2-151282008-T-C

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_004688.3(NMI):ā€‹c.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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.69
Variant links:
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
NMINM_004688.3 linkuse as main transcriptc.117A>G p.Gln39= synonymous_variant 3/8 ENST00000243346.10 NP_004679.2
NMIXM_047446270.1 linkuse as main transcriptc.390A>G p.Gln130= synonymous_variant 3/8 XP_047302226.1
NMIXM_005246941.3 linkuse as main transcriptc.117A>G p.Gln39= synonymous_variant 3/8 XP_005246998.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
NMIENST00000243346.10 linkuse as main transcriptc.117A>G p.Gln39= synonymous_variant 3/81 NM_004688.3 ENSP00000243346 P1
NMIENST00000491771.5 linkuse as main transcriptn.358+860A>G intron_variant, non_coding_transcript_variant 2
NMIENST00000414946.1 linkuse as main transcript downstream_gene_variant 5 ENSP00000387373

Frequencies

GnomAD3 genomes
AF:
0.596
AC:
90442
AN:
151872
Hom.:
27189
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.638
Gnomad AMI
AF:
0.478
Gnomad AMR
AF:
0.663
Gnomad ASJ
AF:
0.506
Gnomad EAS
AF:
0.450
Gnomad SAS
AF:
0.511
Gnomad FIN
AF:
0.598
Gnomad MID
AF:
0.554
Gnomad NFE
AF:
0.578
Gnomad OTH
AF:
0.572
GnomAD3 exomes
AF:
0.572
AC:
140373
AN:
245298
Hom.:
41007
AF XY:
0.563
AC XY:
74638
AN XY:
132514
show subpopulations
Gnomad AFR exome
AF:
0.641
Gnomad AMR exome
AF:
0.706
Gnomad ASJ exome
AF:
0.503
Gnomad EAS exome
AF:
0.439
Gnomad SAS exome
AF:
0.502
Gnomad FIN exome
AF:
0.587
Gnomad NFE exome
AF:
0.567
Gnomad OTH exome
AF:
0.566
GnomAD4 exome
AF:
0.573
AC:
789724
AN:
1378854
Hom.:
228861
Cov.:
23
AF XY:
0.570
AC XY:
393136
AN XY:
690222
show subpopulations
Gnomad4 AFR exome
AF:
0.634
Gnomad4 AMR exome
AF:
0.698
Gnomad4 ASJ exome
AF:
0.502
Gnomad4 EAS exome
AF:
0.483
Gnomad4 SAS exome
AF:
0.503
Gnomad4 FIN exome
AF:
0.584
Gnomad4 NFE exome
AF:
0.576
Gnomad4 OTH exome
AF:
0.562
GnomAD4 genome
AF:
0.596
AC:
90511
AN:
151990
Hom.:
27219
Cov.:
32
AF XY:
0.596
AC XY:
44269
AN XY:
74274
show subpopulations
Gnomad4 AFR
AF:
0.638
Gnomad4 AMR
AF:
0.664
Gnomad4 ASJ
AF:
0.506
Gnomad4 EAS
AF:
0.450
Gnomad4 SAS
AF:
0.512
Gnomad4 FIN
AF:
0.598
Gnomad4 NFE
AF:
0.578
Gnomad4 OTH
AF:
0.565
Alfa
AF:
0.567
Hom.:
55389
Bravo
AF:
0.602
Asia WGS
AF:
0.468
AC:
1629
AN:
3472
EpiCase
AF:
0.556
EpiControl
AF:
0.567

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.94
CADD
Benign
0.86
DANN
Benign
0.27
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs3771886; hg19: chr2-152138522; API