chr2-151288153-T-C

Variant names:

• chr2-151288153-T-C
• rs6734376
• NM_004688.3:c.-7+1440A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_004688.3(NMI):​c.-7+1440A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.261 in 152,162 control chromosomes in the GnomAD database, including 9,261 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 0.26 (9261 hom., cov: 32)
• Consequence: NMI NM_004688.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.225
• Publications: 2 publications found

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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.62 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004688.3. 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.-7+1440A>G		intron	N/A	NP_004679.2	Q13287

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NMI	ENST00000243346.10	TSL:1 MANE Select	c.-7+1440A>G		intron	N/A	ENSP00000243346.5	Q13287
	NMI	ENST00000883657.1		c.-7+738A>G		intron	N/A	ENSP00000553716.1
	NMI	ENST00000883659.1		c.-7+738A>G		intron	N/A	ENSP00000553718.1

Frequencies

GnomAD3 genomes AF: 0.261 AC: 39640 AN: 152044 Hom.: 9239 Cov.: 32

Gnomad AFR AF: 0.627

Gnomad AMI AF: 0.0811

Gnomad AMR AF: 0.165

Gnomad ASJ AF: 0.161

Gnomad EAS AF: 0.0684

Gnomad SAS AF: 0.182

Gnomad FIN AF: 0.0576

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.121

Gnomad OTH AF: 0.227

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.261 AC: 39710 AN: 152162 Hom.: 9261 Cov.: 32 AF XY: 0.254 AC XY: 18872 AN XY: 74380

African (AFR) AF: 0.626 AC: 25959 AN: 41446

American (AMR) AF: 0.165 AC: 2526 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.161 AC: 558 AN: 3470

East Asian (EAS) AF: 0.0685 AC: 355 AN: 5180

South Asian (SAS) AF: 0.183 AC: 882 AN: 4824

European-Finnish (FIN) AF: 0.0576 AC: 611 AN: 10604

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.121 AC: 8211 AN: 68016

Other (OTH) AF: 0.224 AC: 474 AN: 2114

Alfa AF: 0.211 Hom.: 848

Bravo AF: 0.283

Asia WGS AF: 0.158 AC: 552 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	7.8
DANN	Benign	0.83
PhyloP100		-0.23
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs6734376; hg19: chr2-152144667;