rs4307650
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000674696.1(NT5C2):c.-24-25113G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.408 in 152,042 control chromosomes in the GnomAD database, including 12,871 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.41 ( 12871 hom., cov: 32)
Consequence
NT5C2
ENST00000674696.1 intron
ENST00000674696.1 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.285
Genes affected
NT5C2 (HGNC:8022): (5'-nucleotidase, cytosolic II) This gene encodes a hydrolase that serves as an important role in cellular purine metabolism by acting primarily on inosine 5'-monophosphate and other purine nucleotides. [provided by RefSeq, Oct 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.98).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.513 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NT5C2 | ENST00000674696.1 | c.-24-25113G>T | intron_variant | P1 | |||||
NT5C2 | ENST00000675326.1 | c.-168-18767G>T | intron_variant | P1 | |||||
NT5C2 | ENST00000676428.1 | c.-117-2238G>T | intron_variant | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.408 AC: 62022AN: 151924Hom.: 12853 Cov.: 32
GnomAD3 genomes
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62022
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.408 AC: 62086AN: 152042Hom.: 12871 Cov.: 32 AF XY: 0.407 AC XY: 30217AN XY: 74308
GnomAD4 genome
?
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AC:
62086
AN:
152042
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32
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30217
AN XY:
74308
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Asia WGS
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1544
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3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at