Genetic Variant NM_152395.3:c.37C>A (chr3-131381841-C-A) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 0P and 2B. BP4_Moderate

The NM_152395.3(NUDT16):c.37C>A(p.Leu13Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000016 in 1,440,234 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 33)

Exomes 𝑓: 0.000016 ( 0 hom. )

Consequence

NUDT16
NM_152395.3 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: -0.290

Publications

0 publications found

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]

NUDT16 links:

NUDT16-DT (HGNC:27947): (NUDT16 divergent transcript)

NUDT16-DT links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.10050577).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_152395.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
NUDT16	NM_152395.3	MANE Select	c.37C>A	p.Leu13Met	missense	Exon 1 of 3	NP_689608.2	Q96DE0-1
NUDT16	NM_001171906.2		c.37C>A	p.Leu13Met	missense	Exon 1 of 2	NP_001165377.1	Q96DE0-4
NUDT16	NM_001171905.2		c.-1+96C>A		intron	N/A	NP_001165376.1	Q96DE0-3

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
NUDT16	ENST00000521288.2	TSL:1 MANE Select	c.37C>A	p.Leu13Met	missense	Exon 1 of 3	ENSP00000429274.2	Q96DE0-1
NUDT16	ENST00000502852.1	TSL:2	c.37C>A	p.Leu13Met	missense	Exon 1 of 2	ENSP00000422375.1	Q96DE0-4
NUDT16	ENST00000537561.5	TSL:5	c.-1+96C>A		intron	N/A	ENSP00000440230.1	Q96DE0-3

Frequencies

GnomAD3 genomes

Cov.:

GnomAD2 exomes

AF:

0.00

AC:

AN:

213008

AF XY:

0.00

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.0000160

AC:

AN:

1440234

Hom.:

Cov.:

AF XY:

0.0000126

AC XY:

AN XY:

716218

show subpopulations

African (AFR)

AF:

0.000453

AC:

AN:

33140

American (AMR)

AF:

0.00

AC:

AN:

42762

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

25802

East Asian (EAS)

AF:

0.00

AC:

AN:

38958

South Asian (SAS)

AF:

0.00

AC:

AN:

84848

European-Finnish (FIN)

AF:

0.00

AC:

AN:

43822

Middle Eastern (MID)

AF:

0.00

AC:

AN:

4360

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

1106930

Other (OTH)

AF:

0.000134

AC:

AN:

59612

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.477

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

Cov.:

Alfa

AF:

0.00

Hom.:

Bravo

AF:

0.00000378

ClinVar

ClinVar submissions

Significance:Uncertain significance

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not specified (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.14

BayesDel_addAF

Benign

-0.14

BayesDel_noAF

Benign

-0.44

CADD

Benign

8.1

(source)

DANN

Benign

0.76

DEOGEN2

Benign

0.0096

Eigen

Benign

-0.42

Eigen_PC

Benign

-0.54

FATHMM_MKL

Benign

0.35

LIST_S2

Benign

0.45

M_CAP

Benign

0.029

MetaRNN

Benign

0.10

MetaSVM

Benign

-0.97

MutationAssessor

Uncertain

2.1

PhyloP100

-0.29

PrimateAI

Pathogenic

0.79

PROVEAN

Benign

-0.52

REVEL

Benign

0.024

Sift

Benign

0.34

Sift4G

Benign

0.27

Vest4

0.18

MutPred

0.32

Loss of glycosylation at S17 (P = 0.0459)

MVP

0.10

MPC

0.41

ClinPred

0.11

GERP RS

0.75

PromoterAI

0.15

Neutral

(source)

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.6

Varity_R

0.23

gMVP

0.69

Mutation Taster

=77/23

polymorphism

(source)

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over