3-52525097-T-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.1213A>T(p.Met405Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000162 in 1,477,808 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 0.000089 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0000089 ( 0 hom. )
Consequence
NT5DC2
NM_001134231.2 missense
NM_001134231.2 missense
Scores
3
3
13
Clinical Significance
Conservation
PhyloP100: 7.91
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=0.2293311).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NT5DC2 | NM_001134231.2 | c.1213A>T | p.Met405Leu | missense_variant | 12/14 | ENST00000422318.7 | |
NT5DC2 | NM_022908.3 | c.1102A>T | p.Met368Leu | missense_variant | 12/14 | ||
NT5DC2 | XM_006713303.4 | c.1213A>T | p.Met405Leu | missense_variant | 12/14 | ||
NT5DC2 | XM_047448760.1 | c.1102A>T | p.Met368Leu | missense_variant | 12/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NT5DC2 | ENST00000422318.7 | c.1213A>T | p.Met405Leu | missense_variant | 12/14 | 5 | NM_001134231.2 | P2 |
Frequencies
GnomAD3 genomes AF: 0.0000889 AC: 12AN: 135018Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000157 AC: 3AN: 190704Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 104342
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GnomAD4 exome AF: 0.00000894 AC: 12AN: 1342790Hom.: 0 Cov.: 56 AF XY: 0.00000150 AC XY: 1AN XY: 664480
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GnomAD4 genome AF: 0.0000889 AC: 12AN: 135018Hom.: 0 Cov.: 32 AF XY: 0.000125 AC XY: 8AN XY: 64250
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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 | Dec 13, 2022 | The c.1213A>T (p.M405L) alteration is located in exon 12 (coding exon 12) of the NT5DC2 gene. This alteration results from a A to T substitution at nucleotide position 1213, causing the methionine (M) at amino acid position 405 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
Pathogenic
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Benign
DEOGEN2
Benign
T;T;.;.
Eigen
Benign
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Benign
T;T;T;T
M_CAP
Benign
D
MetaRNN
Benign
T;T;T;T
MetaSVM
Benign
T
MutationAssessor
Uncertain
.;M;.;.
MutationTaster
Benign
D;D;D;D
PrimateAI
Pathogenic
D
PROVEAN
Benign
N;N;N;N
REVEL
Benign
Sift
Uncertain
D;D;D;D
Sift4G
Benign
T;T;T;T
Polyphen
0.080
.;B;.;.
Vest4
0.66, 0.65, 0.65
MutPred
0.44
.;Gain of relative solvent accessibility (P = 0.1259);.;.;
MVP
MPC
0.54
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