NM_152395.3:c.205C>G

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2

The NM_152395.3(NUDT16):​c.205C>G​(p.Leu69Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00974 in 1,608,026 control chromosomes in the GnomAD database, including 91 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0071 ( 4 hom., cov: 33)
Exomes 𝑓: 0.010 ( 87 hom. )

Consequence

NUDT16
NM_152395.3 missense

Scores

6
12

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 1.85
Variant links:
Genes affected
NUDT16 (HGNC:26442): (nudix hydrolase 16) Enables several functions, including RNA binding activity; metal ion binding activity; and purine ribonucleoside triphosphate binding activity. Involved in IDP catabolic process; RNA metabolic process; and positive regulation of cell cycle process. Located in cytoplasm; nucleolus; and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.007732898).
BP6
Variant 3-131382112-C-G is Benign according to our data. Variant chr3-131382112-C-G is described in ClinVar as [Benign]. Clinvar id is 783313.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS2
High Homozygotes in GnomAd4 at 4 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
NUDT16NM_152395.3 linkc.205C>G p.Leu69Val missense_variant Exon 2 of 3 ENST00000521288.2 NP_689608.2 Q96DE0-1
NUDT16NM_001171906.2 linkc.205C>G p.Leu69Val missense_variant Exon 2 of 2 NP_001165377.1 Q96DE0-4
NUDT16NM_001171905.2 linkc.67C>G p.Leu23Val missense_variant Exon 2 of 4 NP_001165376.1 Q96DE0-3
NUDT16NR_033268.2 linkn.339C>G non_coding_transcript_exon_variant Exon 1 of 2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
NUDT16ENST00000521288.2 linkc.205C>G p.Leu69Val missense_variant Exon 2 of 3 1 NM_152395.3 ENSP00000429274.2 Q96DE0-1
NUDT16ENST00000502852.1 linkc.205C>G p.Leu69Val missense_variant Exon 2 of 2 2 ENSP00000422375.1 Q96DE0-4
NUDT16ENST00000537561.5 linkc.67C>G p.Leu23Val missense_variant Exon 2 of 4 5 ENSP00000440230.1 Q96DE0-3

Frequencies

GnomAD3 genomes
AF:
0.00715
AC:
1089
AN:
152230
Hom.:
4
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.00207
Gnomad AMI
AF:
0.00877
Gnomad AMR
AF:
0.00583
Gnomad ASJ
AF:
0.0161
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00434
Gnomad FIN
AF:
0.00866
Gnomad MID
AF:
0.0127
Gnomad NFE
AF:
0.0106
Gnomad OTH
AF:
0.00525
GnomAD3 exomes
AF:
0.00794
AC:
1957
AN:
246414
Hom.:
12
AF XY:
0.00822
AC XY:
1099
AN XY:
133740
show subpopulations
Gnomad AFR exome
AF:
0.00232
Gnomad AMR exome
AF:
0.00502
Gnomad ASJ exome
AF:
0.0159
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00435
Gnomad FIN exome
AF:
0.00941
Gnomad NFE exome
AF:
0.0110
Gnomad OTH exome
AF:
0.00702
GnomAD4 exome
AF:
0.0100
AC:
14568
AN:
1455678
Hom.:
87
Cov.:
32
AF XY:
0.00981
AC XY:
7098
AN XY:
723682
show subpopulations
Gnomad4 AFR exome
AF:
0.00159
Gnomad4 AMR exome
AF:
0.00489
Gnomad4 ASJ exome
AF:
0.0162
Gnomad4 EAS exome
AF:
0.0000253
Gnomad4 SAS exome
AF:
0.00411
Gnomad4 FIN exome
AF:
0.00951
Gnomad4 NFE exome
AF:
0.0113
Gnomad4 OTH exome
AF:
0.00883
GnomAD4 genome
AF:
0.00714
AC:
1088
AN:
152348
Hom.:
4
Cov.:
33
AF XY:
0.00664
AC XY:
495
AN XY:
74496
show subpopulations
Gnomad4 AFR
AF:
0.00207
Gnomad4 AMR
AF:
0.00582
Gnomad4 ASJ
AF:
0.0161
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00414
Gnomad4 FIN
AF:
0.00866
Gnomad4 NFE
AF:
0.0106
Gnomad4 OTH
AF:
0.00520
Alfa
AF:
0.0108
Hom.:
4
Bravo
AF:
0.00676
TwinsUK
AF:
0.00971
AC:
36
ALSPAC
AF:
0.0127
AC:
49
ESP6500AA
AF:
0.00227
AC:
10
ESP6500EA
AF:
0.0106
AC:
91
ExAC
AF:
0.00739
AC:
897
Asia WGS
AF:
0.00115
AC:
4
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Benign:2
-
Breakthrough Genomics, Breakthrough Genomics
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: not provided

- -

Nov 03, 2017
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.23
BayesDel_addAF
Benign
-0.55
T
BayesDel_noAF
Benign
-0.55
CADD
Uncertain
24
DANN
Uncertain
1.0
DEOGEN2
Benign
0.012
.;T;.
Eigen
Uncertain
0.23
Eigen_PC
Benign
0.15
FATHMM_MKL
Uncertain
0.79
D
LIST_S2
Uncertain
0.93
D;D;D
MetaRNN
Benign
0.0077
T;T;T
MetaSVM
Benign
-1.1
T
MutationAssessor
Benign
1.8
.;L;L
PrimateAI
Uncertain
0.73
T
PROVEAN
Benign
-2.2
N;N;N
REVEL
Benign
0.092
Sift
Benign
0.074
T;T;T
Sift4G
Uncertain
0.010
D;D;D
Polyphen
1.0
.;D;.
Vest4
0.55
MVP
0.26
MPC
1.3
ClinPred
0.012
T
GERP RS
1.8
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7
Varity_R
0.45
gMVP
0.74

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: rs150437674; hg19: chr3-131100956; COSMIC: COSV99072591; COSMIC: COSV99072591; API