2-151289680-G-C

Position:

• chr2-151289680-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000414946.1(NMI):​c.-281C>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 ENST00000414946.1 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.518

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.151289680G>C		intergenic_region
NMI	NM_004688.3	c.-94C>G		upstream_gene_variant		ENST00000243346.10	NP_004679.2
NMI	XM_005246941.3	c.-796C>G		upstream_gene_variant			XP_005246998.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NMI	ENST00000414946.1	c.-281C>G		5_prime_UTR_variant	1/4	5		ENSP00000387373.1
NMI	ENST00000477072.1	n.184C>G		non_coding_transcript_exon_variant	1/2	3
NMI	ENST00000491771.5	n.184C>G		non_coding_transcript_exon_variant	1/3	2
NMI	ENST00000243346.10	c.-94C>G		upstream_gene_variant		1	NM_004688.3	ENSP00000243346.5

Frequencies

GnomAD3 genomes AF: 0.526 AC: 79961 AN: 151998 Hom.: 21358 Cov.: 33

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: 49 AN: 84 Hom.: 14 Cov.: 0 AF XY: 0.596 AC XY: 31 AN XY: 52

Gnomad4 AFR exome AF: 0.500

Gnomad4 FIN exome AF: 1.00

Gnomad4 NFE exome AF: 0.579

GnomAD4 genome AF: 0.526 AC: 80061 AN: 152116 Hom.: 21410 Cov.: 33 AF XY: 0.530 AC XY: 39391 AN XY: 74354

Gnomad4 AFR AF: 0.589

Gnomad4 AMR AF: 0.588

Gnomad4 ASJ AF: 0.363

Gnomad4 EAS AF: 0.525

Gnomad4 SAS AF: 0.388

Gnomad4 FIN AF: 0.587

Gnomad4 NFE AF: 0.486

Gnomad4 OTH AF: 0.475

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	4.0
DANN	Benign	0.85

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

LitVar

Other links and lift over

dbSNP: rs2194492; hg19: chr2-152146194;