Genetic Variant NUDT11:p.Val66Val (chrX-51496247-C-T) – ACMG Classification: Benign (-9 pts)

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2

The NM_018159.4(NUDT11):c.198G>A(p.Val66Val) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00133 in 1,209,331 control chromosomes in the GnomAD database, including 3 homozygotes. There are 560 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.00083 ( 0 hom., 34 hem., cov: 22)

Exomes 𝑓: 0.0014 ( 3 hom. 526 hem. )

Consequence

NUDT11
NM_018159.4 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.181

Variant links:

Genes affected

NUDT11 (HGNC:18011): (nudix hydrolase 11) NUDT11 belongs to a subgroup of phosphohydrolases that preferentially attack diphosphoinositol polyphosphates (Hidaka et al., 2002 [PubMed 12105228]).[supplied by OMIM, Mar 2008]

NUDT11 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.44).

BP6

Variant X-51496247-C-T is Benign according to our data. Variant chrX-51496247-C-T is described in ClinVar as [Benign]. Clinvar id is 786441.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=0.181 with no splicing effect.

BS2

High Hemizygotes in GnomAd4 at 34 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NUDT11	NM_018159.4 link	c.198G>A	p.Val66Val	synonymous_variant	Exon 1 of 2	ENST00000375992.4	NP_060629.2	Q96G61

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NUDT11	ENST00000375992.4 link	c.198G>A	p.Val66Val	synonymous_variant	Exon 1 of 2	1	NM_018159.4	ENSP00000365160.3		Q96G61

Frequencies

GnomAD3 genomes

AF:

0.000826

AC:

AN:

111335

Hom.:

Cov.:

AF XY:

0.00101

AC XY:

AN XY:

33499

show subpopulations

Gnomad AFR

AF:

0.000163

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0000946

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000390

Gnomad FIN

AF:

0.00630

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000887

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.00149

AC:

272

AN:

182307

Hom.:

AF XY:

0.00146

AC XY:

AN XY:

67353

show subpopulations

Gnomad AFR exome

AF:

0.000233

Gnomad AMR exome

AF:

0.0000730

Gnomad ASJ exome

AF:

0.000268

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00105

Gnomad FIN exome

AF:

0.00795

Gnomad NFE exome

AF:

0.00138

Gnomad OTH exome

AF:

0.00134

GnomAD4 exome

AF:

0.00138

AC:

1518

AN:

1097942

Hom.:

Cov.:

AF XY:

0.00145

AC XY:

526

AN XY:

363416

show subpopulations

Gnomad4 AFR exome

AF:

0.000152

Gnomad4 AMR exome

AF:

0.0000852

Gnomad4 ASJ exome

AF:

0.000206

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000961

Gnomad4 FIN exome

AF:

0.00649

Gnomad4 NFE exome

AF:

0.00137

Gnomad4 OTH exome

AF:

0.000695

GnomAD4 genome

AF:

0.000826

AC:

AN:

111389

Hom.:

Cov.:

AF XY:

0.00101

AC XY:

AN XY:

33563

show subpopulations

Gnomad4 AFR

AF:

0.000163

Gnomad4 AMR

AF:

0.0000945

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000391

Gnomad4 FIN

AF:

0.00630

Gnomad4 NFE

AF:

0.000887

Gnomad4 OTH

AF:

0.00

Alfa

AF:

0.000400

Hom.:

Bravo

AF:

0.000514

EpiCase

AF:

0.00131

EpiControl

AF:

0.00160

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Jul 18, 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_noAF

Benign

-0.44

CADD

Benign

DANN

Benign

0.81

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.070

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