NM_002520.7:c.495C>T
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_002520.7(NPM1):c.495C>T(p.Asp165Asp) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000634 in 1,607,674 control chromosomes in the GnomAD database, including 9 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_002520.7 synonymous
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NPM1 | NM_002520.7 | c.495C>T | p.Asp165Asp | synonymous_variant | Exon 6 of 11 | ENST00000296930.10 | NP_002511.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00312 AC: 474AN: 151768Hom.: 4 Cov.: 32
GnomAD3 exomes AF: 0.000777 AC: 194AN: 249570Hom.: 1 AF XY: 0.000555 AC XY: 75AN XY: 135162
GnomAD4 exome AF: 0.000374 AC: 544AN: 1455788Hom.: 5 Cov.: 32 AF XY: 0.000315 AC XY: 228AN XY: 724590
GnomAD4 genome AF: 0.00313 AC: 476AN: 151886Hom.: 4 Cov.: 32 AF XY: 0.00272 AC XY: 202AN XY: 74220
ClinVar
Submissions by phenotype
not provided Benign:1
- -
NPM1-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at