dbSNP rs289831: NMI:c.178-10T>C (chr2-151279000-A-G) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The NM_004688.3(NMI):c.178-10T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.133 in 1,543,842 control chromosomes in the GnomAD database, including 17,070 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 0.19 ( 3768 hom., cov: 32)

Exomes 𝑓: 0.13 ( 13302 hom. )

Consequence

NMI
NM_004688.3 intron

Scores

Splicing: ADA: 0.004861

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.10

Publications

16 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 -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.39).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.363 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein
NMI	NM_004688.3 link	c.178-10T>C	intron_variant	Intron 3 of 7	ENST00000243346.10	NP_004679.2
NMI	XM_047446270.1 link	c.451-10T>C	intron_variant	Intron 3 of 7		XP_047302226.1
NMI	XM_005246941.3 link	c.178-10T>C	intron_variant	Intron 3 of 7		XP_005246998.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NMI	ENST00000243346.10 link	c.178-10T>C		intron_variant	Intron 3 of 7	1	NM_004688.3	ENSP00000243346.5
NMI	ENST00000491771.5 link	n.359-10T>C		intron_variant	Intron 2 of 2	2

Frequencies

GnomAD3 genomes

AF:

0.190

AC:

28868

AN:

152050

Hom.:

3763

Cov.:

show subpopulations

Gnomad AFR

AF:

0.368

Gnomad AMI

AF:

0.0811

Gnomad AMR

AF:

0.139

Gnomad ASJ

AF:

0.169

Gnomad EAS

AF:

0.127

Gnomad SAS

AF:

0.200

Gnomad FIN

AF:

0.0577

Gnomad MID

AF:

0.177

Gnomad NFE

AF:

0.121

Gnomad OTH

AF:

0.181

GnomAD2 exomes

AF:

0.137

AC:

32045

AN:

233598

AF XY:

0.138

show subpopulations

Gnomad AFR exome

AF:

0.368

Gnomad AMR exome

AF:

0.0852

Gnomad ASJ exome

AF:

0.168

Gnomad EAS exome

AF:

0.128

Gnomad FIN exome

AF:

0.0594

Gnomad NFE exome

AF:

0.117

Gnomad OTH exome

AF:

0.129

GnomAD4 exome

AF:

0.127

AC:

176519

AN:

1391674

Hom.:

13302

Cov.:

AF XY:

0.129

AC XY:

89325

AN XY:

690870

show subpopulations

African (AFR)

AF:

0.368

AC:

11529

AN:

31364

American (AMR)

AF:

0.0893

AC:

3667

AN:

41058

Ashkenazi Jewish (ASJ)

AF:

0.168

AC:

4225

AN:

25212

East Asian (EAS)

AF:

0.123

AC:

4803

AN:

38892

South Asian (SAS)

AF:

0.199

AC:

16224

AN:

81722

European-Finnish (FIN)

AF:

0.0635

AC:

3296

AN:

51924

Middle Eastern (MID)

AF:

0.237

AC:

1310

AN:

5532

European-Non Finnish (NFE)

AF:

0.116

AC:

122901

AN:

1058302

Other (OTH)

AF:

0.149

AC:

8564

AN:

57668

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.482

Heterozygous variant carriers

6525

13050

19574

26099

32624

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

4624

9248

13872

18496

23120

<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:

0.190

AC:

28908

AN:

152168

Hom.:

3768

Cov.:

AF XY:

0.186

AC XY:

13820

AN XY:

74406

show subpopulations

African (AFR)

AF:

0.368

AC:

15257

AN:

41476

American (AMR)

AF:

0.138

AC:

2114

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.169

AC:

588

AN:

3470

East Asian (EAS)

AF:

0.127

AC:

658

AN:

5176

South Asian (SAS)

AF:

0.201

AC:

968

AN:

4826

European-Finnish (FIN)

AF:

0.0577

AC:

612

AN:

10614

Middle Eastern (MID)

AF:

0.184

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.121

AC:

8205

AN:

68008

Other (OTH)

AF:

0.179

AC:

378

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1101

2202

3303

4404

5505

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

302

604

906

1208

1510

<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:

0.141

Hom.:

1071

Bravo

AF:

0.200

Asia WGS

AF:

0.188

AC:

654

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.39

CADD

Benign

(source)

DANN

Benign

0.79

PhyloP100

2.1

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.0049

dbscSNV1_RF

Benign

0.23

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

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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