rs73353837
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_001351169.2(NT5C2):c.634-89G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00333 in 1,009,286 control chromosomes in the GnomAD database, including 67 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.013 ( 41 hom., cov: 32)
Exomes 𝑓: 0.0016 ( 26 hom. )
Consequence
NT5C2
NM_001351169.2 intron
NM_001351169.2 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.319
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 -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BP6
Variant 10-103099073-C-T is Benign according to our data. Variant chr10-103099073-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 1209471.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0128 (1953/152218) while in subpopulation AFR AF= 0.0429 (1780/41522). AF 95% confidence interval is 0.0412. There are 41 homozygotes in gnomad4. There are 908 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 41 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NT5C2 | NM_001351169.2 | c.634-89G>A | intron_variant | ENST00000404739.8 | NP_001338098.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NT5C2 | ENST00000404739.8 | c.634-89G>A | intron_variant | 1 | NM_001351169.2 | ENSP00000383960.3 |
Frequencies
GnomAD3 genomes AF: 0.0128 AC: 1952AN: 152100Hom.: 41 Cov.: 32
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GnomAD4 exome AF: 0.00164 AC: 1406AN: 857068Hom.: 26 AF XY: 0.00143 AC XY: 632AN XY: 443310
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GnomAD4 genome AF: 0.0128 AC: 1953AN: 152218Hom.: 41 Cov.: 32 AF XY: 0.0122 AC XY: 908AN XY: 74412
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 06, 2019 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at