Genetic Variant NUTM2F:p.Arg515Pro (chr9-94319192-C-G) – ACMG Classification: Likely_benign (-4 pts)

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_017561.2(NUTM2F):c.1544G>C(p.Arg515Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 16/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.000090 ( 0 hom., cov: 12)

Exomes 𝑓: 0.000011 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

NUTM2F
NM_017561.2 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 0.714

Publications

2 publications found

Variant links:

Genes affected

NUTM2F (HGNC:23450): (NUT family member 2F)

NUTM2F links:

LOC105376154 (HGNC:):

LOC105376154 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -4 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.006900698).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_017561.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NUTM2F	NM_017561.2	MANE Select	c.1544G>C	p.Arg515Pro	missense	Exon 7 of 7	NP_060031.1	A1L443

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NUTM2F	ENST00000253262.9	TSL:1 MANE Select	c.1544G>C	p.Arg515Pro	missense	Exon 7 of 7	ENSP00000253262.4	A1L443

Frequencies

GnomAD3 genomes

AF:

0.0000900

AC:

AN:

100012

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000380

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00

Gnomad OTH

AF:

0.00

GnomAD2 exomes

AF:

0.0000357

AC:

AN:

83994

AF XY:

0.0000230

show subpopulations

Gnomad AFR exome

AF:

0.000343

Gnomad AMR exome

AF:

0.0000723

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

Data not reliable, filtered out with message: AS_VQSR

AF:

0.0000113

AC:

AN:

1060446

Hom.:

Cov.:

AF XY:

0.00000946

AC XY:

AN XY:

528634

show subpopulations

African (AFR)

AF:

0.000321

AC:

AN:

24886

American (AMR)

AF:

0.0000641

AC:

AN:

31184

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

21130

East Asian (EAS)

AF:

0.00

AC:

AN:

33688

South Asian (SAS)

AF:

0.00

AC:

AN:

65122

European-Finnish (FIN)

AF:

0.00

AC:

AN:

44538

Middle Eastern (MID)

AF:

0.00

AC:

AN:

3418

European-Non Finnish (NFE)

AF:

0.00000127

AC:

AN:

790176

Other (OTH)

AF:

0.0000216

AC:

AN:

46304

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.567

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

Data not reliable, filtered out with message: AS_VQSR

AF:

0.0000899

AC:

AN:

100108

Hom.:

Cov.:

AF XY:

0.0000648

AC XY:

AN XY:

46274

show subpopulations

African (AFR)

AF:

0.000378

AC:

AN:

23800

American (AMR)

AF:

0.00

AC:

AN:

8906

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

2770

East Asian (EAS)

AF:

0.00

AC:

AN:

3480

South Asian (SAS)

AF:

0.00

AC:

AN:

2390

European-Finnish (FIN)

AF:

0.00

AC:

AN:

6720

Middle Eastern (MID)

AF:

0.00

AC:

AN:

256

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

49746

Other (OTH)

AF:

0.00

AC:

AN:

1284

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.647

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome 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

Alfa

AF:

0.00

Hom.:

ExAC

AF:

0.0000694

AC:

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

0.11

BayesDel_addAF

Benign

-0.55

BayesDel_noAF

Benign

-0.71

CADD

Benign

(source)

DANN

Benign

0.89

DEOGEN2

Benign

0.0019

Eigen

Benign

-1.1

Eigen_PC

Benign

-1.2

FATHMM_MKL

Benign

0.0054

LIST_S2

Benign

0.62

M_CAP

Benign

0.0019

MetaRNN

Benign

0.0069

MetaSVM

Benign

-0.99

MutationAssessor

Benign

0.69

PhyloP100

0.71

PrimateAI

Benign

0.44

PROVEAN

Benign

-0.59

REVEL

Benign

0.019

Sift

Benign

0.070

Sift4G

Uncertain

0.037

Polyphen

0.46

Vest4

0.16

MutPred

0.33

Loss of MoRF binding (P = 6e-04)

MVP

0.014

ClinPred

0.030

GERP RS

-2.2

Varity_R

0.11

gMVP

0.045

Mutation Taster

=98/2

polymorphism

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over