dbSNP rs11730: NMI:c.*196T>C (chr2-151270497-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_004688.3(NMI):c.*196T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.413 in 563,072 control chromosomes in the GnomAD database, including 52,132 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 0.36 ( 12074 hom., cov: 33)

Exomes 𝑓: 0.43 ( 40058 hom. )

Consequence

NMI
NM_004688.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.248

Publications

19 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:

Genome browser will be placed here

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=-0.87).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.496 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein
NMI	NM_004688.3 link	c.*196T>C	3_prime_UTR_variant	Exon 8 of 8	ENST00000243346.10	NP_004679.2
NMI	XM_047446270.1 link	c.*196T>C	3_prime_UTR_variant	Exon 8 of 8		XP_047302226.1
NMI	XM_005246941.3 link	c.*196T>C	3_prime_UTR_variant	Exon 8 of 8		XP_005246998.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NMI	ENST00000243346.10 link	c.*196T>C		3_prime_UTR_variant	Exon 8 of 8	1	NM_004688.3	ENSP00000243346.5

Frequencies

GnomAD3 genomes

AF:

0.362

AC:

54990

AN:

152064

Hom.:

12063

Cov.:

show subpopulations

Gnomad AFR

AF:

0.109

Gnomad AMI

AF:

0.398

Gnomad AMR

AF:

0.504

Gnomad ASJ

AF:

0.340

Gnomad EAS

AF:

0.382

Gnomad SAS

AF:

0.325

Gnomad FIN

AF:

0.548

Gnomad MID

AF:

0.367

Gnomad NFE

AF:

0.456

Gnomad OTH

AF:

0.361

GnomAD4 exome

AF:

0.432

AC:

177523

AN:

410890

Hom.:

40058

Cov.:

AF XY:

0.426

AC XY:

92294

AN XY:

216726

show subpopulations

African (AFR)

AF:

0.119

AC:

1318

AN:

11114

American (AMR)

AF:

0.554

AC:

8051

AN:

14526

Ashkenazi Jewish (ASJ)

AF:

0.337

AC:

4289

AN:

12732

East Asian (EAS)

AF:

0.426

AC:

12023

AN:

28222

South Asian (SAS)

AF:

0.319

AC:

11778

AN:

36968

European-Finnish (FIN)

AF:

0.526

AC:

13873

AN:

26356

Middle Eastern (MID)

AF:

0.316

AC:

585

AN:

1852

European-Non Finnish (NFE)

AF:

0.454

AC:

115840

AN:

255122

Other (OTH)

AF:

0.407

AC:

9766

AN:

23998

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.511

Heterozygous variant carriers

4630

9260

13891

18521

23151

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

610

1220

1830

2440

3050

<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:

0.361

AC:

54997

AN:

152182

Hom.:

12074

Cov.:

AF XY:

0.368

AC XY:

27379

AN XY:

74398

show subpopulations

African (AFR)

AF:

0.108

AC:

4500

AN:

41536

American (AMR)

AF:

0.505

AC:

7722

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.340

AC:

1179

AN:

3468

East Asian (EAS)

AF:

0.381

AC:

1973

AN:

5178

South Asian (SAS)

AF:

0.325

AC:

1567

AN:

4828

European-Finnish (FIN)

AF:

0.548

AC:

5796

AN:

10568

Middle Eastern (MID)

AF:

0.374

AC:

110

AN:

294

European-Non Finnish (NFE)

AF:

0.456

AC:

31033

AN:

67998

Other (OTH)

AF:

0.357

AC:

754

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1637

3274

4912

6549

8186

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

522

1044

1566

2088

2610

<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:

0.424

Hom.:

18393

Bravo

AF:

0.349

Asia WGS

AF:

0.316

AC:

1101

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

2.3

(source)

DANN

Benign

0.50

PhyloP100

0.25

Mutation Taster

=100/0

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over