5-171392976-A-G
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_ModerateBP6BP7BS1BS2
The NM_002520.7(NPM1):āc.522A>Gā(p.Glu174=) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00135 in 1,609,544 control chromosomes in the GnomAD database, including 50 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (no stars).
Frequency
Consequence
NM_002520.7 splice_region, synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NPM1 | NM_002520.7 | c.522A>G | p.Glu174= | splice_region_variant, synonymous_variant | 6/11 | ENST00000296930.10 | NP_002511.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NPM1 | ENST00000296930.10 | c.522A>G | p.Glu174= | splice_region_variant, synonymous_variant | 6/11 | 1 | NM_002520.7 | ENSP00000296930 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000795 AC: 121AN: 152200Hom.: 3 Cov.: 33
GnomAD3 exomes AF: 0.00299 AC: 737AN: 246284Hom.: 16 AF XY: 0.00396 AC XY: 529AN XY: 133444
GnomAD4 exome AF: 0.00141 AC: 2058AN: 1457226Hom.: 47 Cov.: 32 AF XY: 0.00207 AC XY: 1503AN XY: 725126
GnomAD4 genome AF: 0.000788 AC: 120AN: 152318Hom.: 3 Cov.: 33 AF XY: 0.00101 AC XY: 75AN XY: 74480
ClinVar
Submissions by phenotype
not specified Benign:1
Benign, no assertion criteria provided | clinical testing | Genetic Services Laboratory, University of Chicago | Jun 06, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at