Genetic Variant 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

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	UniProt
NMI	NM_004688.3 link	c.178-10T>C	intron_variant	Intron 3 of 7	ENST00000243346.10	NP_004679.2	Q13287
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	Q13287

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		Q13287
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

Gnomad4 AFR exome

AF:

0.368

AC:

11529

AN:

31364

Gnomad4 AMR exome

AF:

0.0893

AC:

3667

AN:

41058

Gnomad4 ASJ exome

AF:

0.168

AC:

4225

AN:

25212

Gnomad4 EAS exome

AF:

0.123

AC:

4803

AN:

38892

Gnomad4 SAS exome

AF:

0.199

AC:

16224

AN:

81722

Gnomad4 FIN exome

AF:

0.0635

AC:

3296

AN:

51924

Gnomad4 NFE exome

AF:

0.116

AC:

122901

AN:

1058302

Gnomad4 Remaining exome

AF:

0.149

AC:

8564

AN:

57668

Heterozygous variant carriers

6525

13050

19574

26099

32624

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

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

Gnomad4 AFR

AF:

0.368

AC:

0.367851

AN:

0.367851

Gnomad4 AMR

AF:

0.138

AC:

0.138351

AN:

0.138351

Gnomad4 ASJ

AF:

0.169

AC:

0.169452

AN:

0.169452

Gnomad4 EAS

AF:

0.127

AC:

0.127125

AN:

0.127125

Gnomad4 SAS

AF:

0.201

AC:

0.20058

AN:

0.20058

Gnomad4 FIN

AF:

0.0577

AC:

0.0576597

AN:

0.0576597

Gnomad4 NFE

AF:

0.121

AC:

0.120648

AN:

0.120648

Gnomad4 OTH

AF:

0.179

AC:

0.178977

AN:

0.178977

Heterozygous variant carriers

1101

2202

3303

4404

5505

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

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

DANN

Benign

0.79

Mutation Taster

=100/0

polymorphism (auto)

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

LitVar

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

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over