3-52524854-C-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.1375G>T(p.Val459Leu) variant causes a missense change. The variant allele was found at a frequency of 0.0000682 in 1,612,248 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 0.000033 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000072 ( 0 hom. )
Consequence
NT5DC2
NM_001134231.2 missense
NM_001134231.2 missense
Scores
4
15
Clinical Significance
Conservation
PhyloP100: 4.51
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=0.20518488).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NT5DC2 | NM_001134231.2 | c.1375G>T | p.Val459Leu | missense_variant | 13/14 | ENST00000422318.7 | |
NT5DC2 | NM_022908.3 | c.1264G>T | p.Val422Leu | missense_variant | 13/14 | ||
NT5DC2 | XM_006713303.4 | c.1375G>T | p.Val459Leu | missense_variant | 13/14 | ||
NT5DC2 | XM_047448760.1 | c.1264G>T | p.Val422Leu | missense_variant | 13/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NT5DC2 | ENST00000422318.7 | c.1375G>T | p.Val459Leu | missense_variant | 13/14 | 5 | NM_001134231.2 | P2 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152132Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000205 AC: 5AN: 244436Hom.: 0 AF XY: 0.0000226 AC XY: 3AN XY: 132926
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GnomAD4 exome AF: 0.0000719 AC: 105AN: 1460116Hom.: 0 Cov.: 70 AF XY: 0.0000578 AC XY: 42AN XY: 726358
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GnomAD4 genome AF: 0.0000329 AC: 5AN: 152132Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74318
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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 | Feb 07, 2023 | The c.1375G>T (p.V459L) alteration is located in exon 13 (coding exon 13) of the NT5DC2 gene. This alteration results from a G to T substitution at nucleotide position 1375, causing the valine (V) at amino acid position 459 to be replaced by a leucine (L). 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
Uncertain
DANN
Benign
DEOGEN2
Benign
T;T;.;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;D;D;D
M_CAP
Benign
T
MetaRNN
Benign
T;T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
.;L;.;.
MutationTaster
Benign
D;D;D;D
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N;N;N
REVEL
Benign
Sift
Benign
T;T;T;T
Sift4G
Benign
T;T;T;T
Polyphen
0.0020
.;B;.;.
Vest4
0.35, 0.34, 0.35
MutPred
0.57
.;Loss of MoRF binding (P = 0.1028);.;.;
MVP
MPC
0.41
ClinPred
T
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