Genetic Variant NUTM2F:p.Arg515Gln (chr9-94319192-C-T) – 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>A(p.Arg515Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R515P) has been classified as Uncertain significance.

Frequency

Genomes: 𝑓 0.0012 ( 0 hom., cov: 12)

Exomes 𝑓: 0.00022 ( 1 hom. )

Failed GnomAD Quality Control

Consequence

NUTM2F
NM_017561.2 missense

Scores

Clinical Significance

Not reported in ClinVar

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=0.0036925077).

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>A	p.Arg515Gln	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>A	p.Arg515Gln	missense	Exon 7 of 7	ENSP00000253262.4	A1L443

Frequencies

GnomAD3 genomes

AF:

0.00121

AC:

121

AN:

100006

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00481

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000562

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:

0.00157

GnomAD2 exomes

AF:

0.000714

AC:

AN:

83994

AF XY:

0.000551

show subpopulations

Gnomad AFR exome

AF:

0.00943

Gnomad AMR exome

AF:

0.000362

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:

0.000222

AC:

235

AN:

1060414

Hom.:

Cov.:

AF XY:

0.000189

AC XY:

100

AN XY:

528620

show subpopulations

African (AFR)

AF:

0.00760

AC:

189

AN:

24868

American (AMR)

AF:

0.000385

AC:

AN:

31180

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

21130

East Asian (EAS)

AF:

0.00

AC:

AN:

33688

South Asian (SAS)

AF:

0.0000154

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:

0.0000152

AC:

AN:

790172

Other (OTH)

AF:

0.000454

AC:

AN:

46298

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.404

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

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:

0.00120

AC:

120

AN:

100100

Hom.:

Cov.:

AF XY:

0.00112

AC XY:

AN XY:

46268

show subpopulations

African (AFR)

AF:

0.00475

AC:

113

AN:

23792

American (AMR)

AF:

0.000561

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:

0.00156

AC:

AN:

1284

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.432

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:

0.000131

Hom.:

ExAC

AF:

0.0000925

AC:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.088

BayesDel_addAF

Benign

-0.71

BayesDel_noAF

Benign

-0.79

CADD

Benign

(source)

DANN

Uncertain

0.98

DEOGEN2

Benign

0.0019

Eigen

Benign

-1.1

Eigen_PC

Benign

-1.2

FATHMM_MKL

Benign

0.0029

LIST_S2

Benign

0.72

MetaRNN

Benign

0.0037

MetaSVM

Benign

-0.99

MutationAssessor

Benign

0.69

PhyloP100

0.71

PrimateAI

Benign

0.41

PROVEAN

Benign

0.30

REVEL

Benign

0.028

Sift

Benign

0.13

Sift4G

Uncertain

0.056

Polyphen

0.48

Vest4

0.081

MVP

0.014

ClinPred

0.011

GERP RS

-2.2

Varity_R

0.029

gMVP

0.033

Mutation Taster

=100/0

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

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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