chr13-48045719-C-T
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_018283.4(NUDT15):c.415C>T(p.Arg139Cys) variant causes a missense change. The variant allele was found at a frequency of 0.0117 in 1,612,064 control chromosomes in the GnomAD database, including 632 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as drug response (★★★).
Frequency
Consequence
NM_018283.4 missense
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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NUDT15 | NM_018283.4 | c.415C>T | p.Arg139Cys | missense_variant | Exon 3 of 3 | ENST00000258662.3 | NP_060753.1 | |
NUDT15 | NR_136687.2 | n.436C>T | non_coding_transcript_exon_variant | Exon 3 of 5 | ||||
NUDT15 | NR_136688.2 | n.436C>T | non_coding_transcript_exon_variant | Exon 3 of 5 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0126 AC: 1908AN: 152016Hom.: 66 Cov.: 32
GnomAD3 exomes AF: 0.0282 AC: 7054AN: 249720Hom.: 276 AF XY: 0.0281 AC XY: 3798AN XY: 135108
GnomAD4 exome AF: 0.0117 AC: 17014AN: 1459930Hom.: 565 Cov.: 30 AF XY: 0.0129 AC XY: 9382AN XY: 726348
GnomAD4 genome AF: 0.0126 AC: 1912AN: 152134Hom.: 67 Cov.: 32 AF XY: 0.0146 AC XY: 1086AN XY: 74362
ClinVar
Submissions by phenotype
NUDT15-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Thiopurines, poor metabolism of, 2 Other:1
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azathioprine response - Toxicity Other:1
PharmGKB Level of Evidence 1A: Level 1A clinical annotations describe variant-drug combinations that have variant-specific prescribing guidance available in a current clinical guideline annotation or an FDA-approved drug label annotation. Annotations of drug labels or clinical guidelines must give prescribing guidance for specific variants (e.g. CYP2C9*3, HLA-B*57:01) or provide mapping from defined allele functions to diplotypes and phenotypes to be used as supporting evidence for a level 1A clinical annotation. Level 1A clinical annotations must also be supported by at least one publication in addition to a clinical guideline or drug label with variant-specific prescribing guidance. Drug-variant association: Toxicity
mercaptopurine response - Dosage Other:1
PharmGKB Level of Evidence 1A: Level 1A clinical annotations describe variant-drug combinations that have variant-specific prescribing guidance available in a current clinical guideline annotation or an FDA-approved drug label annotation. Annotations of drug labels or clinical guidelines must give prescribing guidance for specific variants (e.g. CYP2C9*3, HLA-B*57:01) or provide mapping from defined allele functions to diplotypes and phenotypes to be used as supporting evidence for a level 1A clinical annotation. Level 1A clinical annotations must also be supported by at least one publication in addition to a clinical guideline or drug label with variant-specific prescribing guidance. Drug-variant association: Dosage
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at