NM_006545.5:c.*59delG
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1
The NM_006545.5(NPRL2):c.*59delG variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0404 in 1,596,450 control chromosomes in the GnomAD database, including 12,239 homozygotes. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_006545.5 3_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NPRL2 | NM_006545.5 | c.*59delG | 3_prime_UTR_variant | Exon 11 of 11 | ENST00000232501.8 | NP_006536.3 | ||
NPRL2 | XM_047447310.1 | c.*59delG | 3_prime_UTR_variant | Exon 11 of 11 | XP_047303266.1 | |||
NPRL2 | XM_011533288.4 | c.*59delG | 3_prime_UTR_variant | Exon 10 of 10 | XP_011531590.1 | |||
NPRL2 | XM_017005556.3 | c.*59delG | 3_prime_UTR_variant | Exon 9 of 9 | XP_016861045.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0872 AC: 13238AN: 151852Hom.: 1897 Cov.: 31
GnomAD4 exome AF: 0.0355 AC: 51304AN: 1444480Hom.: 10341 Cov.: 28 AF XY: 0.0322 AC XY: 23192AN XY: 719758
GnomAD4 genome AF: 0.0873 AC: 13263AN: 151970Hom.: 1898 Cov.: 31 AF XY: 0.0936 AC XY: 6953AN XY: 74262
ClinVar
Submissions by phenotype
not specified Benign:1
This variant is classified as Benign based on local population frequency. This variant was detected in 45% of patients studied in a panel designed for Epileptic and Developmental Encephalopathy, Progressive Myoclonus Epilepsy and Abnormal Movements and Neurodegeneration with brain iron accumulation. Number of patients: 42. Only high quality variants are reported. -
not provided Benign:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at