chr3-52525069-G-A

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001134231.2(NT5DC2):​c.1241C>T​(p.Ala414Val) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000398 in 1,590,486 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A414T) has been classified as Uncertain significance.

Frequency

Genomes: 𝑓 0.00029 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00041 ( 0 hom. )

Consequence

NT5DC2
NM_001134231.2 missense

Scores

6
8
5

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 9.86
Variant links:
Genes affected
NT5DC2 (HGNC:25717): (5'-nucleotidase domain containing 2) Predicted to enable 5'-nucleotidase activity. Predicted to be involved in dephosphorylation. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

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
NT5DC2NM_001134231.2 linkuse as main transcriptc.1241C>T p.Ala414Val missense_variant 12/14 ENST00000422318.7
NT5DC2NM_022908.3 linkuse as main transcriptc.1130C>T p.Ala377Val missense_variant 12/14
NT5DC2XM_006713303.4 linkuse as main transcriptc.1241C>T p.Ala414Val missense_variant 12/14
NT5DC2XM_047448760.1 linkuse as main transcriptc.1130C>T p.Ala377Val missense_variant 12/14

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
NT5DC2ENST00000422318.7 linkuse as main transcriptc.1241C>T p.Ala414Val missense_variant 12/145 NM_001134231.2 P2Q9H857-2

Frequencies

GnomAD3 genomes
AF:
0.000290
AC:
44
AN:
151736
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0000727
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0000656
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000574
Gnomad OTH
AF:
0.000480
GnomAD3 exomes
AF:
0.000213
AC:
43
AN:
202010
Hom.:
0
AF XY:
0.000207
AC XY:
23
AN XY:
110996
show subpopulations
Gnomad AFR exome
AF:
0.0000920
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000469
Gnomad OTH exome
AF:
0.000194
GnomAD4 exome
AF:
0.000409
AC:
589
AN:
1438750
Hom.:
0
Cov.:
57
AF XY:
0.000402
AC XY:
287
AN XY:
713996
show subpopulations
Gnomad4 AFR exome
AF:
0.000213
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.0000201
Gnomad4 NFE exome
AF:
0.000513
Gnomad4 OTH exome
AF:
0.000269
GnomAD4 genome
AF:
0.000290
AC:
44
AN:
151736
Hom.:
0
Cov.:
32
AF XY:
0.000283
AC XY:
21
AN XY:
74090
show subpopulations
Gnomad4 AFR
AF:
0.0000727
Gnomad4 AMR
AF:
0.0000656
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000574
Gnomad4 OTH
AF:
0.000480
Alfa
AF:
0.000418
Hom.:
0
Bravo
AF:
0.000246
ESP6500AA
AF:
0.00
AC:
0
ESP6500EA
AF:
0.000350
AC:
3
ExAC
AF:
0.000134
AC:
16

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 submitterclinical testingAmbry GeneticsAug 02, 2021The c.1241C>T (p.A414V) alteration is located in exon 12 (coding exon 12) of the NT5DC2 gene. This alteration results from a C to T substitution at nucleotide position 1241, causing the alanine (A) at amino acid position 414 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.98
BayesDel_addAF
Uncertain
0.016
T
BayesDel_noAF
Uncertain
0.12
CADD
Pathogenic
29
DANN
Pathogenic
1.0
DEOGEN2
Benign
0.050
T;T;.;.
Eigen
Pathogenic
0.79
Eigen_PC
Pathogenic
0.74
FATHMM_MKL
Pathogenic
0.98
D
LIST_S2
Pathogenic
1.0
D;D;D;D
M_CAP
Benign
0.075
D
MetaRNN
Uncertain
0.71
D;D;D;D
MetaSVM
Benign
-0.76
T
MutationAssessor
Uncertain
2.5
.;M;.;.
MutationTaster
Benign
1.0
D;D;D;D
PrimateAI
Uncertain
0.79
T
PROVEAN
Uncertain
-4.0
D;D;D;D
REVEL
Uncertain
0.51
Sift
Benign
0.069
T;D;D;D
Sift4G
Uncertain
0.038
D;T;D;D
Polyphen
0.98
.;D;.;.
Vest4
0.95, 0.95, 0.92
MVP
0.58
MPC
0.89
ClinPred
0.74
D
GERP RS
5.1
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7
Varity_R
0.46
gMVP
0.91

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: rs201549406; hg19: chr3-52559085; API