chr3-52525259-G-A
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Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001134231.2(NT5DC2):c.1156C>T(p.Arg386Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000539 in 1,612,618 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000013 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000058 ( 0 hom. )
Consequence
NT5DC2
NM_001134231.2 missense
NM_001134231.2 missense
Scores
5
5
9
Clinical Significance
Conservation
PhyloP100: 2.60
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NT5DC2 | NM_001134231.2 | c.1156C>T | p.Arg386Cys | missense_variant | 11/14 | ENST00000422318.7 | |
NT5DC2 | NM_022908.3 | c.1045C>T | p.Arg349Cys | missense_variant | 11/14 | ||
NT5DC2 | XM_006713303.4 | c.1156C>T | p.Arg386Cys | missense_variant | 11/14 | ||
NT5DC2 | XM_047448760.1 | c.1045C>T | p.Arg349Cys | missense_variant | 11/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NT5DC2 | ENST00000422318.7 | c.1156C>T | p.Arg386Cys | missense_variant | 11/14 | 5 | NM_001134231.2 | P2 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152098Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000281 AC: 7AN: 249374Hom.: 0 AF XY: 0.0000222 AC XY: 3AN XY: 135342
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GnomAD4 exome AF: 0.0000582 AC: 85AN: 1460520Hom.: 0 Cov.: 32 AF XY: 0.0000551 AC XY: 40AN XY: 726544
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GnomAD4 genome AF: 0.0000131 AC: 2AN: 152098Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74284
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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 | Sep 26, 2022 | The c.1156C>T (p.R386C) alteration is located in exon 11 (coding exon 11) of the NT5DC2 gene. This alteration results from a C to T substitution at nucleotide position 1156, causing the arginine (R) at amino acid position 386 to be replaced by a cysteine (C). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
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
Pathogenic
D;D;D;D
M_CAP
Uncertain
D
MetaRNN
Uncertain
D;D;D;D
MetaSVM
Benign
T
MutationAssessor
Pathogenic
.;M;.;.
MutationTaster
Benign
D;D;D;D
PrimateAI
Pathogenic
D
PROVEAN
Pathogenic
D;D;D;D
REVEL
Benign
Sift
Benign
T;D;D;D
Sift4G
Benign
T;T;T;T
Polyphen
0.98
.;D;.;.
Vest4
0.73, 0.74, 0.69
MutPred
0.65
.;Loss of solvent accessibility (P = 0.0329);.;.;
MVP
MPC
1.3
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