Genetic Variant NMI:c.-796C>G (chr2-151289680-G-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000883657.1(NMI):c.-796C>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 0.526 in 152,200 control chromosomes in the GnomAD database, including 21,424 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: 𝑓 0.53 ( 21410 hom., cov: 33)

Exomes 𝑓: 0.58 ( 14 hom. )

Consequence

NMI
ENST00000883657.1 5_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.518

Publications

11 publications found

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]

NMI links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.78).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.583 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000883657.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NMI	NM_004688.3	MANE Select	c.-94C>G		upstream_gene	N/A	NP_004679.2	Q13287

Ensembl Transcripts

Gene	Transcript	HGVSc	Effect	Exon Rank	Protein
NMI	ENST00000883657.1	c.-796C>G	5_prime_UTR	Exon 1 of 8	ENSP00000553716.1
NMI	ENST00000883656.1	c.-94C>G	5_prime_UTR	Exon 1 of 7	ENSP00000553715.1
NMI	ENST00000883658.1	c.-94C>G	5_prime_UTR	Exon 1 of 6	ENSP00000553717.1

Frequencies

GnomAD3 genomes

AF:

0.526

AC:

79961

AN:

151998

Hom.:

21358

Cov.:

show subpopulations

Gnomad AFR

AF:

0.589

Gnomad AMI

AF:

0.419

Gnomad AMR

AF:

0.587

Gnomad ASJ

AF:

0.363

Gnomad EAS

AF:

0.525

Gnomad SAS

AF:

0.388

Gnomad FIN

AF:

0.587

Gnomad MID

AF:

0.405

Gnomad NFE

AF:

0.486

Gnomad OTH

AF:

0.483

GnomAD4 exome

AF:

0.583

AC:

AN:

Hom.:

Cov.:

AF XY:

0.596

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.500

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

1.00

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.579

AC:

AN:

Other (OTH)

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.496

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.526

AC:

80061

AN:

152116

Hom.:

21410

Cov.:

AF XY:

0.530

AC XY:

39391

AN XY:

74354

show subpopulations

African (AFR)

AF:

0.589

AC:

24454

AN:

41486

American (AMR)

AF:

0.588

AC:

8993

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.363

AC:

1260

AN:

3468

East Asian (EAS)

AF:

0.525

AC:

2715

AN:

5172

South Asian (SAS)

AF:

0.388

AC:

1874

AN:

4824

European-Finnish (FIN)

AF:

0.587

AC:

6215

AN:

10582

Middle Eastern (MID)

AF:

0.418

AC:

123

AN:

294

European-Non Finnish (NFE)

AF:

0.486

AC:

33042

AN:

67976

Other (OTH)

AF:

0.475

AC:

1003

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1997

3994

5990

7987

9984

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

700

1400

2100

2800

3500

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.520

Hom.:

2539

Bravo

AF:

0.534

Asia WGS

AF:

0.441

AC:

1536

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.78

CADD

Benign

4.0

(source)

DANN

Benign

0.85

PhyloP100

-0.52

PromoterAI

-0.14

Neutral

(source)

Mutation Taster

=300/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over