NM_002520.7(NPM1):c.864_873delinsTTTAAGGATTCGTC (p.Trp288fs) AND Acute myeloid leukemia with multilineage dysplasia

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jan 7, 2020
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV000999466.1

Allele description [Variation Report for NM_002520.7(NPM1):c.864_873delinsTTTAAGGATTCGTC (p.Trp288fs)]

NM_002520.7(NPM1):c.864_873delinsTTTAAGGATTCGTC (p.Trp288fs)

Gene:

NPM1:nucleophosmin 1 [Gene - OMIM - HGNC]

Variant type:

Indel

Cytogenetic location:

5q35.1

Genomic location:

Preferred name:

NM_002520.7(NPM1):c.864_873delinsTTTAAGGATTCGTC (p.Trp288fs)

HGVS:

NC_000005.10:g.171410544_171410553delinsTTTAAGGATTCGTC
NG_016018.1:g.27841_27850delinsTTTAAGGATTCGTC
NM_001355006.2:c.864_873delinsTTTAAGGATTCGTC
NM_001355007.2:c.672_681delinsTTTAAGGATTCGTC
NM_001355010.2:c.483_492delinsTTTAAGGATTCGTC
NM_002520.7:c.864_873delinsTTTAAGGATTCGTCMANE SELECT
NM_199185.4:c.777_786delinsTTTAAGGATTCGTC
NP_001341935.1:p.Trp288fs
NP_001341936.1:p.Trp224fs
NP_001341939.1:p.Trp161fs
NP_002511.1:p.Trp288fs
NP_002511.1:p.Trp288fs
NP_954654.1:p.Trp259fs
LRG_458t1:c.864_873delinsTTTAAGGATTCGTC
LRG_458:g.27841_27850delinsTTTAAGGATTCGTC
LRG_458p1:p.Trp288fs
NC_000005.9:g.170837548_170837557delinsTTTAAGGATTCGTC
NM_002520.6:c.864_873delinsTTTAAGGATTCGTC
NR_149149.2:n.836_845delinsTTTAAGGATTCGTC

Protein change:

W161fs

Links:

dbSNP: rs1581263026

NCBI 1000 Genomes Browser:

rs1581263026

Molecular consequence:

NM_001355006.2:c.864_873delinsTTTAAGGATTCGTC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001355007.2:c.672_681delinsTTTAAGGATTCGTC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001355010.2:c.483_492delinsTTTAAGGATTCGTC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_002520.7:c.864_873delinsTTTAAGGATTCGTC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_199185.4:c.777_786delinsTTTAAGGATTCGTC - frameshift variant - [Sequence Ontology: SO:0001589]
NR_149149.2:n.836_845delinsTTTAAGGATTCGTC - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Functional consequence:

protein truncation [Variation Ontology: 0015]

Observations:

Condition(s)

Name:: Acute myeloid leukemia with multilineage dysplasia
Identifiers:: MONDO: MONDO:0019456; MedGen: C1292773

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001134991	Molecular Haematology Laboratory, NSW Health Pathology	no assertion criteria provided	Pathogenic (Jan 7, 2020)	somatic	clinical testing

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001134991

Molecular Haematology Laboratory, NSW Health Pathology

no assertion criteria provided

Pathogenic
(Jan 7, 2020)

somatic

clinical testing

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	somatic	yes	1	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From Molecular Haematology Laboratory, NSW Health Pathology, SCV001134991.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1		1	not provided	not provided	clinical testing	not provided

Description

Variant was not detected 12 months earlier when first diagnosed with myelodysplastic syndrome.

Description

The locus of the mutation is in the mutational hotspot for NPM1 mutations in acute myeloid leukemia and results in a frameshift [NM_002520.6(NPM1_i001):p.(Trp288Cysfs*12)] with the same loss of protein domain as other NPM1 mutations identified in hematological malignancies.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	somatic	yes	not provided	not provided	not provided		1	not provided	not provided	not provided

Last Updated: Apr 23, 2022

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