rs12262171
Positions:
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 2P and 10B. PM2BP4_StrongBP6_ModerateBS1
The NM_001351169.2(NT5C2):āc.407A>Gā(p.Gln136Arg) variant causes a missense change. The variant allele was found at a frequency of 0.000131 in 1,599,476 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Genomes: š 0.00075 ( 0 hom., cov: 32)
Exomes š: 0.000066 ( 0 hom. )
Consequence
NT5C2
NM_001351169.2 missense
NM_001351169.2 missense
Scores
2
16
Clinical Significance
Conservation
PhyloP100: 3.62
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 -8 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (MetaRNN=0.010461003).
BP6
?
Variant 10-103101309-T-C is Benign according to our data. Variant chr10-103101309-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 474946.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.000749 (114/152292) while in subpopulation AFR AF= 0.00265 (110/41562). AF 95% confidence interval is 0.00225. There are 0 homozygotes in gnomad4. There are 58 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NT5C2 | NM_001351169.2 | c.407A>G | p.Gln136Arg | missense_variant | 7/19 | ENST00000404739.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NT5C2 | ENST00000404739.8 | c.407A>G | p.Gln136Arg | missense_variant | 7/19 | 1 | NM_001351169.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000749 AC: 114AN: 152174Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000205 AC: 51AN: 248608Hom.: 0 AF XY: 0.000141 AC XY: 19AN XY: 134462
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GnomAD4 exome AF: 0.0000656 AC: 95AN: 1447184Hom.: 0 Cov.: 27 AF XY: 0.0000541 AC XY: 39AN XY: 720628
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GnomAD4 genome ? AF: 0.000749 AC: 114AN: 152292Hom.: 0 Cov.: 32 AF XY: 0.000779 AC XY: 58AN XY: 74470
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Asia WGS
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Hereditary spastic paraplegia 45 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 06, 2023 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
DEOGEN2
Benign
T;T;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
M_CAP
Benign
T
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
N;N;.
MutationTaster
Benign
D;D;D
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N;N
REVEL
Benign
Sift
Benign
T;T;T
Sift4G
Benign
T;T;T
Polyphen
B;B;.
Vest4
MVP
MPC
0.74
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at