Variant rs34351976 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_002520.7(NPM1):c.*165del variant causes a 3 prime UTR change. The variant allele was found at a frequency of 0.326 in 509,706 control chromosomes in the GnomAD database, including 29,164 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.28 ( 6957 hom., cov: 21)

Exomes 𝑓: 0.35 ( 22207 hom. )

Consequence

NPM1
NM_002520.7 3_prime_UTR

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 4.83

Variant links:

Genes affected

NPM1 (HGNC:7910): (nucleophosmin 1) The protein encoded by this gene is involved in several cellular processes, including centrosome duplication, protein chaperoning, and cell proliferation. The encoded phosphoprotein shuttles between the nucleolus, nucleus, and cytoplasm, chaperoning ribosomal proteins and core histones from the nucleus to the cytoplasm. This protein is also known to sequester the tumor suppressor ARF in the nucleolus, protecting it from degradation until it is needed. Mutations in this gene are associated with acute myeloid leukemia. Dozens of pseudogenes of this gene have been identified. [provided by RefSeq, Aug 2017]

NPM1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.414 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NPM1	NM_002520.7 linkuse as main transcript	c.*165del		3_prime_UTR_variant	11/11	ENST00000296930.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NPM1	ENST00000296930.10 linkuse as main transcript	c.*165del		3_prime_UTR_variant	11/11	1	NM_002520.7	P1	P06748-1

Frequencies

GnomAD3 genomes

AF:

0.282

AC:

42762

AN:

151790

Hom.:

6956

Cov.:

show subpopulations

Gnomad AFR

AF:

0.115

Gnomad AMI

AF:

0.510

Gnomad AMR

AF:

0.237

Gnomad ASJ

AF:

0.373

Gnomad EAS

AF:

0.428

Gnomad SAS

AF:

0.372

Gnomad FIN

AF:

0.354

Gnomad MID

AF:

0.278

Gnomad NFE

AF:

0.356

Gnomad OTH

AF:

0.316

GnomAD4 exome

AF:

0.345

AC:

123500

AN:

357798

Hom.:

22207

Cov.:

AF XY:

0.348

AC XY:

65400

AN XY:

188166

show subpopulations

Gnomad4 AFR exome

AF:

0.117

Gnomad4 AMR exome

AF:

0.218

Gnomad4 ASJ exome

AF:

0.370

Gnomad4 EAS exome

AF:

0.427

Gnomad4 SAS exome

AF:

0.351

Gnomad4 FIN exome

AF:

0.359

Gnomad4 NFE exome

AF:

0.349

Gnomad4 OTH exome

AF:

0.331

GnomAD4 genome

AF:

0.281

AC:

42761

AN:

151908

Hom.:

6957

Cov.:

AF XY:

0.281

AC XY:

20842

AN XY:

74232

show subpopulations

Gnomad4 AFR

AF:

0.114

Gnomad4 AMR

AF:

0.237

Gnomad4 ASJ

AF:

0.373

Gnomad4 EAS

AF:

0.429

Gnomad4 SAS

AF:

0.373

Gnomad4 FIN

AF:

0.354

Gnomad4 NFE

AF:

0.356

Gnomad4 OTH

AF:

0.313

Alfa

AF:

0.206

Hom.:

530

Bravo

AF:

0.264

Asia WGS

AF:

0.322

AC:

1120

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over