NM_152395.3:c.205C>G
Variant names:
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
NM_152395.3 missense
Scores
6
12
Clinical Significance
Conservation
PhyloP100: 1.85
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]
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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 |
---|---|---|---|---|---|---|---|---|
NUDT16 | NM_152395.3 | c.205C>G | p.Leu69Val | missense_variant | Exon 2 of 3 | ENST00000521288.2 | NP_689608.2 | |
NUDT16 | NM_001171906.2 | c.205C>G | p.Leu69Val | missense_variant | Exon 2 of 2 | NP_001165377.1 | ||
NUDT16 | NM_001171905.2 | c.67C>G | p.Leu23Val | missense_variant | Exon 2 of 4 | NP_001165376.1 | ||
NUDT16 | NR_033268.2 | n.339C>G | non_coding_transcript_exon_variant | Exon 1 of 2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NUDT16 | ENST00000521288.2 | c.205C>G | p.Leu69Val | missense_variant | Exon 2 of 3 | 1 | NM_152395.3 | ENSP00000429274.2 | ||
NUDT16 | ENST00000502852.1 | c.205C>G | p.Leu69Val | missense_variant | Exon 2 of 2 | 2 | ENSP00000422375.1 | |||
NUDT16 | ENST00000537561.5 | c.67C>G | p.Leu23Val | missense_variant | Exon 2 of 4 | 5 | ENSP00000440230.1 |
Frequencies
GnomAD3 genomes AF: 0.00715 AC: 1089AN: 152230Hom.: 4 Cov.: 33
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GnomAD3 exomes AF: 0.00794 AC: 1957AN: 246414Hom.: 12 AF XY: 0.00822 AC XY: 1099AN XY: 133740
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GnomAD4 exome AF: 0.0100 AC: 14568AN: 1455678Hom.: 87 Cov.: 32 AF XY: 0.00981 AC XY: 7098AN XY: 723682
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GnomAD4 genome AF: 0.00714 AC: 1088AN: 152348Hom.: 4 Cov.: 33 AF XY: 0.00664 AC XY: 495AN XY: 74496
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ESP6500AA
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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:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Benign
.;T;.
Eigen
Uncertain
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;D;D
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
.;L;L
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N;N
REVEL
Benign
Sift
Benign
T;T;T
Sift4G
Uncertain
D;D;D
Polyphen
1.0
.;D;.
Vest4
MVP
MPC
1.3
ClinPred
T
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