ENST00000911790.1:c.-5+151T>G

Variant names:

• chr17-51153191-T-G
• rs3760469
• ENST00000911790.1:c.-5+151T>G

Variant summary

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

The ENST00000911790.1(NME1):​c.-5+151T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.547 in 152,090 control chromosomes in the GnomAD database, including 23,493 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 0.55 (23493 hom., cov: 33)
• Consequence: NME1 ENST00000911790.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.398
• Publications: 12 publications found

Genes affected

NME1 (HGNC:7849): (NME/NM23 nucleoside diphosphate kinase 1) This gene (NME1) was identified because of its reduced mRNA transcript levels in highly metastatic cells. Nucleoside diphosphate kinase (NDK) exists as a hexamer composed of 'A' (encoded by this gene) and 'B' (encoded by NME2) isoforms. Mutations in this gene have been identified in aggressive neuroblastomas. Two transcript variants encoding different isoforms have been found for this gene. Co-transcription of this gene and the neighboring downstream gene (NME2) generates naturally-occurring transcripts (NME1-NME2), which encodes a fusion protein comprised of sequence sharing identity with each individual gene product. [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=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.687 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000911790.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NME1	ENST00000911790.1		c.-5+151T>G		intron	N/A	ENSP00000581849.1

Frequencies

GnomAD3 genomes AF: 0.547 AC: 83096 AN: 151972 Hom.: 23464 Cov.: 33

Gnomad AFR AF: 0.693

Gnomad AMI AF: 0.514

Gnomad AMR AF: 0.511

Gnomad ASJ AF: 0.474

Gnomad EAS AF: 0.398

Gnomad SAS AF: 0.357

Gnomad FIN AF: 0.487

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.505

Gnomad OTH AF: 0.528

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

GnomAD4 genome AF: 0.547 AC: 83177 AN: 152090 Hom.: 23493 Cov.: 33 AF XY: 0.540 AC XY: 40179 AN XY: 74350

African (AFR) AF: 0.693 AC: 28767 AN: 41484

American (AMR) AF: 0.510 AC: 7779 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.474 AC: 1646 AN: 3472

East Asian (EAS) AF: 0.398 AC: 2064 AN: 5188

South Asian (SAS) AF: 0.358 AC: 1726 AN: 4826

European-Finnish (FIN) AF: 0.487 AC: 5138 AN: 10558

Middle Eastern (MID) AF: 0.480 AC: 141 AN: 294

European-Non Finnish (NFE) AF: 0.505 AC: 34325 AN: 67996

Other (OTH) AF: 0.531 AC: 1122 AN: 2114

Alfa AF: 0.508 Hom.: 20776

Bravo AF: 0.559

Asia WGS AF: 0.416 AC: 1445 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.57
PhyloP100		-0.40
PromoterAI		-0.014	Neutral

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs3760469; hg19: chr17-49230552;