2-151270497-A-G

Variant names:

• chr2-151270497-A-G
• rs11730
• NM_004688.3:c.*196T>C

Variant summary

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

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.248
• Publications: 19 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=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.496 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NMI	NM_004688.3	MANE Select	c.*196T>C		3_prime_UTR	Exon 8 of 8	NP_004679.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NMI	ENST00000243346.10	TSL:1 MANE Select	c.*196T>C		3_prime_UTR	Exon 8 of 8	ENSP00000243346.5

Frequencies

GnomAD3 genomes AF: 0.362 AC: 54990 AN: 152064 Hom.: 12063 Cov.: 33

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.: 4 AF XY: 0.426 AC XY: 92294 AN XY: 216726

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

GnomAD4 genome AF: 0.361 AC: 54997 AN: 152182 Hom.: 12074 Cov.: 33 AF XY: 0.368 AC XY: 27379 AN XY: 74398

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

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.3
DANN	Benign	0.50
PhyloP100		0.25
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: rs11730; hg19: chr2-152127011;