chr3-52527332-G-A
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Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001134231.2(NT5DC2):c.1081C>T(p.Arg361Trp) variant causes a missense change. The variant allele was found at a frequency of 0.0000217 in 1,614,114 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000046 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000019 ( 0 hom. )
Consequence
NT5DC2
NM_001134231.2 missense
NM_001134231.2 missense
Scores
2
9
8
Clinical Significance
Conservation
PhyloP100: 5.64
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.17579526).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NT5DC2 | NM_001134231.2 | c.1081C>T | p.Arg361Trp | missense_variant | 10/14 | ENST00000422318.7 | |
NT5DC2 | NM_022908.3 | c.970C>T | p.Arg324Trp | missense_variant | 10/14 | ||
NT5DC2 | XM_006713303.4 | c.1081C>T | p.Arg361Trp | missense_variant | 10/14 | ||
NT5DC2 | XM_047448760.1 | c.970C>T | p.Arg324Trp | missense_variant | 10/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NT5DC2 | ENST00000422318.7 | c.1081C>T | p.Arg361Trp | missense_variant | 10/14 | 5 | NM_001134231.2 | P2 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152192Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000598 AC: 15AN: 250990Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135854
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GnomAD4 exome AF: 0.0000192 AC: 28AN: 1461804Hom.: 0 Cov.: 31 AF XY: 0.0000206 AC XY: 15AN XY: 727200
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GnomAD4 genome AF: 0.0000460 AC: 7AN: 152310Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74496
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 31, 2023 | The c.1081C>T (p.R361W) alteration is located in exon 10 (coding exon 10) of the NT5DC2 gene. This alteration results from a C to T substitution at nucleotide position 1081, causing the arginine (R) at amino acid position 361 to be replaced by a tryptophan (W). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Pathogenic
DANN
Pathogenic
DEOGEN2
Benign
T;T;.;.
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;D;D;D
M_CAP
Benign
D
MetaRNN
Benign
T;T;T;T
MetaSVM
Benign
T
MutationAssessor
Uncertain
.;M;.;.
MutationTaster
Benign
D;D;D;D
PrimateAI
Uncertain
T
PROVEAN
Pathogenic
D;D;D;D
REVEL
Benign
Sift
Uncertain
D;D;D;D
Sift4G
Uncertain
D;D;D;D
Polyphen
1.0
.;D;.;.
Vest4
0.50, 0.51, 0.48
MVP
MPC
1.1
ClinPred
D
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
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