rs200207416

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_002526.4(NT5E):​c.400G>A​(p.Glu134Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. E134Q) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 32)

Consequence

NT5E
NM_002526.4 missense

Scores

19

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.393
Variant links:
Genes affected
NT5E (HGNC:8021): (5'-nucleotidase ecto) The protein encoded by this gene is a plasma membrane protein that catalyzes the conversion of extracellular nucleotides to membrane-permeable nucleosides. The encoded protein is used as a determinant of lymphocyte differentiation. Defects in this gene can lead to the calcification of joints and arteries. Two transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Mar 2011]

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.06791806).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
NT5ENM_002526.4 linkc.400G>A p.Glu134Lys missense_variant Exon 2 of 9 ENST00000257770.8 NP_002517.1 P21589-1Q6NZX3
NT5ENM_001204813.2 linkc.400G>A p.Glu134Lys missense_variant Exon 2 of 8 NP_001191742.1 P21589-2Q6NZX3

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
NT5EENST00000257770.8 linkc.400G>A p.Glu134Lys missense_variant Exon 2 of 9 1 NM_002526.4 ENSP00000257770.3 P21589-1
NT5EENST00000369646.7 linkc.400G>A p.Glu134Lys missense_variant Exon 2 of 3 1 ENSP00000358660.3 Q96B60
NT5EENST00000369651.7 linkc.400G>A p.Glu134Lys missense_variant Exon 2 of 8 2 ENSP00000358665.3 P21589-2

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
32
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.092
BayesDel_addAF
Benign
-0.16
T
BayesDel_noAF
Benign
-0.46
CADD
Benign
6.7
DANN
Benign
0.45
DEOGEN2
Benign
0.31
.;.;T
Eigen
Benign
-1.1
Eigen_PC
Benign
-1.0
FATHMM_MKL
Benign
0.042
N
LIST_S2
Benign
0.77
T;T;T
M_CAP
Benign
0.019
T
MetaRNN
Benign
0.068
T;T;T
MetaSVM
Benign
-0.92
T
MutationAssessor
Benign
0.60
N;.;N
PrimateAI
Benign
0.29
T
PROVEAN
Benign
-0.47
N;N;N
REVEL
Benign
0.17
Sift
Benign
0.28
T;T;T
Sift4G
Benign
0.33
T;T;T
Polyphen
0.0020, 0.0010
.;B;B
Vest4
0.23
MutPred
0.40
Loss of helix (P = 0.079);Loss of helix (P = 0.079);Loss of helix (P = 0.079);
MVP
0.67
MPC
0.20
ClinPred
0.046
T
GERP RS
-1.3
Varity_R
0.17
gMVP
0.72

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs200207416; hg19: chr6-86176838; COSMIC: COSV57628519; COSMIC: COSV57628519; API