rs34475806
Your query was ambiguous. Multiple possible variants found:
- chr5-171392586-CTTTTTTT-C
- chr5-171392586-CTTTTTTT-CT
- chr5-171392586-CTTTTTTT-CTT
- chr5-171392586-CTTTTTTT-CTTT
- chr5-171392586-CTTTTTTT-CTTTT
- chr5-171392586-CTTTTTTT-CTTTTT
- chr5-171392586-CTTTTTTT-CTTTTTT
- chr5-171392586-CTTTTTTT-CTTTTTTTT
- chr5-171392586-CTTTTTTT-CTTTTTTTTT
- chr5-171392586-CTTTTTTT-CTTTTTTTTTT
- chr5-171392586-CTTTTTTT-CTTTTTTTTTTT
- chr5-171392586-CTTTTTTT-CTTTTTTTTTTTT
- chr5-171392586-CTTTTTTT-CTTTTTTTTTTTTT
Variant summary
Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2
The NM_002520.7(NPM1):c.353-113_353-107delTTTTTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000443 in 451,254 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0000070 ( 0 hom., cov: 0)
Exomes 𝑓: 0.0000032 ( 0 hom. )
Consequence
NPM1
NM_002520.7 intron
NM_002520.7 intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.08
Publications
0 publications found
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 Gene-Disease associations (from GenCC):
- dyskeratosis congenitaInheritance: AD Classification: STRONG, SUPPORTIVE Submitted by: Orphanet, G2P
- bone marrow failure syndromeInheritance: AD Classification: LIMITED Submitted by: ClinGen
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_002520.7. 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 |
|---|---|---|---|---|---|---|---|---|---|
| NPM1 | NM_002520.7 | MANE Select | c.353-113_353-107delTTTTTTT | intron | N/A | NP_002511.1 | A0A0S2Z491 | ||
| NPM1 | NM_001355006.2 | c.353-113_353-107delTTTTTTT | intron | N/A | NP_001341935.1 | A0A0S2Z491 | |||
| NPM1 | NM_199185.4 | c.353-113_353-107delTTTTTTT | intron | N/A | NP_954654.1 | P06748-2 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| NPM1 | ENST00000296930.10 | TSL:1 MANE Select | c.353-123_353-117delTTTTTTT | intron | N/A | ENSP00000296930.5 | P06748-1 | ||
| NPM1 | ENST00000517671.5 | TSL:1 | c.353-123_353-117delTTTTTTT | intron | N/A | ENSP00000428755.1 | P06748-1 | ||
| NPM1 | ENST00000351986.10 | TSL:1 | c.353-123_353-117delTTTTTTT | intron | N/A | ENSP00000341168.6 | P06748-2 |
Frequencies
GnomAD3 genomes 0.00000701 AC: 1AN: 142632Hom.: 0 Cov.: 0 show subpopulations
GnomAD3 genomes
AF:
AC:
1
AN:
142632
Hom.:
Cov.:
0
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.00000324 AC: 1AN: 308622Hom.: 0 AF XY: 0.00000627 AC XY: 1AN XY: 159420 show subpopulations
GnomAD4 exome
AF:
AC:
1
AN:
308622
Hom.:
AF XY:
AC XY:
1
AN XY:
159420
show subpopulations
African (AFR)
AF:
AC:
0
AN:
7546
American (AMR)
AF:
AC:
0
AN:
9200
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
9200
East Asian (EAS)
AF:
AC:
0
AN:
22418
South Asian (SAS)
AF:
AC:
0
AN:
14306
European-Finnish (FIN)
AF:
AC:
0
AN:
20984
Middle Eastern (MID)
AF:
AC:
0
AN:
1338
European-Non Finnish (NFE)
AF:
AC:
1
AN:
205800
Other (OTH)
AF:
AC:
0
AN:
17830
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.825
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
0
2
4
6
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10
<30
30-35
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Age
GnomAD4 genome 0.00000701 AC: 1AN: 142632Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 69006 show subpopulations
GnomAD4 genome
AF:
AC:
1
AN:
142632
Hom.:
Cov.:
0
AF XY:
AC XY:
0
AN XY:
69006
show subpopulations
African (AFR)
AF:
AC:
1
AN:
38830
American (AMR)
AF:
AC:
0
AN:
14312
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3378
East Asian (EAS)
AF:
AC:
0
AN:
4940
South Asian (SAS)
AF:
AC:
0
AN:
4570
European-Finnish (FIN)
AF:
AC:
0
AN:
8210
Middle Eastern (MID)
AF:
AC:
0
AN:
296
European-Non Finnish (NFE)
AF:
AC:
0
AN:
65274
Other (OTH)
AF:
AC:
0
AN:
1942
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.675
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
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>80
Age
Alfa
AF:
Hom.:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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