2-151286035-G-T

Variant names:

• chr2-151286035-G-T
• rs11683487
• NM_004688.3:c.-6-3081C>A

Variant summary

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

The NM_004688.3(NMI):​c.-6-3081C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.36 in 151,926 control chromosomes in the GnomAD database, including 12,028 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 (12028 hom., cov: 32)
• Consequence: NMI NM_004688.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0620
• Publications: 6 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.497 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NMI	NM_004688.3	c.-6-3081C>A		intron_variant	Intron 1 of 7	ENST00000243346.10	NP_004679.2
NMI	XM_005246941.3	c.-7+2856C>A		intron_variant	Intron 1 of 7		XP_005246998.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NMI	ENST00000243346.10	c.-6-3081C>A		intron_variant	Intron 1 of 7	1	NM_004688.3	ENSP00000243346.5
NMI	ENST00000414946.1	c.-7+2856C>A		intron_variant	Intron 2 of 3	5		ENSP00000387373.1
NMI	ENST00000477072.1	n.272-3081C>A		intron_variant	Intron 1 of 1	3
NMI	ENST00000491771.5	n.272-3081C>A		intron_variant	Intron 1 of 2	2

Frequencies

GnomAD3 genomes AF: 0.361 AC: 54760 AN: 151808 Hom.: 12017 Cov.: 32

Gnomad AFR AF: 0.105

Gnomad AMI AF: 0.398

Gnomad AMR AF: 0.505

Gnomad ASJ AF: 0.343

Gnomad EAS AF: 0.381

Gnomad SAS AF: 0.328

Gnomad FIN AF: 0.540

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.458

Gnomad OTH AF: 0.363

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

GnomAD4 genome AF: 0.360 AC: 54767 AN: 151926 Hom.: 12028 Cov.: 32 AF XY: 0.367 AC XY: 27232 AN XY: 74244

African (AFR) AF: 0.104 AC: 4327 AN: 41460

American (AMR) AF: 0.506 AC: 7726 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.343 AC: 1191 AN: 3468

East Asian (EAS) AF: 0.381 AC: 1965 AN: 5162

South Asian (SAS) AF: 0.328 AC: 1575 AN: 4802

European-Finnish (FIN) AF: 0.540 AC: 5674 AN: 10514

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.458 AC: 31081 AN: 67936

Other (OTH) AF: 0.358 AC: 755 AN: 2110

Alfa AF: 0.293 Hom.: 850

Bravo AF: 0.348

Asia WGS AF: 0.316 AC: 1101 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.68
DANN	Benign	0.26
PhyloP100		-0.062
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: rs11683487; hg19: chr2-152142549;