Genetic Variant NUDT16:c.408+179G>A (chr3-131382494-G-A) – ACMG Classification: Benign (-16 pts)

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1

The NM_001171906.2(NUDT16):c.587G>A(p.Trp196*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00763 in 1,536,168 control chromosomes in the GnomAD database, including 722 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.039 ( 404 hom., cov: 33)

Exomes 𝑓: 0.0042 ( 318 hom. )

Consequence

NUDT16
NM_001171906.2 stop_gained

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.0390

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP6

Variant 3-131382494-G-A is Benign according to our data. Variant chr3-131382494-G-A is described in ClinVar as [Benign]. Clinvar id is 770147.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.133 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NUDT16	NM_152395.3 link	c.408+179G>A		intron_variant	Intron 2 of 2	ENST00000521288.2	NP_689608.2	Q96DE0-1
NUDT16	NM_001171906.2 link	c.587G>A	p.Trp196*	stop_gained	Exon 2 of 2		NP_001165377.1	Q96DE0-4
NUDT16	NM_001171905.2 link	c.270+179G>A		intron_variant	Intron 2 of 3		NP_001165376.1	Q96DE0-3
NUDT16	NR_033268.2 link	n.542+179G>A		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
NUDT16	ENST00000521288.2 link	c.408+179G>A		intron_variant	Intron 2 of 2	1	NM_152395.3	ENSP00000429274.2	Q96DE0-1
NUDT16	ENST00000502852.1 link	c.587G>A	p.Trp196*	stop_gained	Exon 2 of 2	2		ENSP00000422375.1	Q96DE0-4
NUDT16	ENST00000537561.5 link	c.270+179G>A		intron_variant	Intron 2 of 3	5		ENSP00000440230.1	Q96DE0-3

Frequencies

GnomAD3 genomes

AF:

0.0392

AC:

5959

AN:

152140

Hom.:

404

Cov.:

show subpopulations

Gnomad AFR

AF:

0.136

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0139

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00104

Gnomad FIN

AF:

0.000189

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.000456

Gnomad OTH

AF:

0.0277

GnomAD3 exomes

AF:

0.00794

AC:

1072

AN:

135006

Hom.:

AF XY:

0.00617

AC XY:

454

AN XY:

73558

show subpopulations

Gnomad AFR exome

AF:

0.131

Gnomad AMR exome

AF:

0.00735

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000133

Gnomad FIN exome

AF:

0.000185

Gnomad NFE exome

AF:

0.000452

Gnomad OTH exome

AF:

0.00434

GnomAD4 exome

AF:

0.00416

AC:

5752

AN:

1383910

Hom.:

318

Cov.:

AF XY:

0.00361

AC XY:

2463

AN XY:

682918

show subpopulations

Gnomad4 AFR exome

AF:

0.139

Gnomad4 AMR exome

AF:

0.00860

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000341

Gnomad4 FIN exome

AF:

0.000501

Gnomad4 NFE exome

AF:

0.000415

Gnomad4 OTH exome

AF:

0.00934

GnomAD4 genome

AF:

0.0392

AC:

5974

AN:

152258

Hom.:

404

Cov.:

AF XY:

0.0372

AC XY:

2771

AN XY:

74450

show subpopulations

Gnomad4 AFR

AF:

0.136

Gnomad4 AMR

AF:

0.0139

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000623

Gnomad4 FIN

AF:

0.000189

Gnomad4 NFE

AF:

0.000456

Gnomad4 OTH

AF:

0.0274

Alfa

AF:

0.0121

Hom.:

Bravo

AF:

0.0441

TwinsUK

AF:

0.00

AC:

ALSPAC

AF:

0.000519

AC:

ExAC

AF:

0.00440

AC:

214

Asia WGS

AF:

0.00635

AC:

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

- -

Aug 16, 2018

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

BayesDel_addAF

Benign

-0.19

BayesDel_noAF

Uncertain

0.070

CADD

Benign

5.5

DANN

Benign

0.72

Eigen

Benign

0.054

Eigen_PC

Benign

-0.39

FATHMM_MKL

Benign

0.0074

Vest4

0.024

GERP RS

0.20

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over