dbSNP rs531076919: NUTM2E:p.Ala457Asp (chr10-79848531-C-A) – ACMG Classification: Likely_benign (-6 pts)

Variant summary

Our verdict is Likely benign. The variant received -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate

The NM_001355263.2(NUTM2E):c.1370C>A(p.Ala457Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.000091 ( 1 hom., cov: 0)

Exomes 𝑓: 0.00043 ( 85 hom. )

Failed GnomAD Quality Control

Consequence

NUTM2E
NM_001355263.2 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.0290

Publications

1 publications found

Variant links:

Genes affected

NUTM2E (HGNC:23448): (NUT family member 2E)

NUTM2E links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -6 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.00750196).

BP6

Variant 10-79848531-C-A is Benign according to our data. Variant chr10-79848531-C-A is described in ClinVar as Likely_benign. ClinVar VariationId is 2640648.Status of the report is criteria_provided_single_submitter, 1 stars.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001355263.2. 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
	NUTM2E	NM_001355263.2	MANE Select	c.1370C>A	p.Ala457Asp	missense	Exon 8 of 10	NP_001342192.1	B1AL46

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NUTM2E	ENST00000429984.5	TSL:5 MANE Select	c.1370C>A	p.Ala457Asp	missense	Exon 8 of 10	ENSP00000407521.2	B1AL46
	NUTM2E	ENST00000602967.5	TSL:5	c.1370C>A	p.Ala457Asp	missense	Exon 5 of 6	ENSP00000473558.1	R4GNA6

Frequencies

GnomAD3 genomes

AF:

0.0000912

AC:

AN:

43846

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00254

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00

Gnomad OTH

AF:

0.00

GnomAD2 exomes

AF:

0.000464

AC:

AN:

73248

AF XY:

0.000613

show subpopulations

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:

0.000490

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.000429

AC:

212

AN:

493648

Hom.:

Cov.:

AF XY:

0.000602

AC XY:

151

AN XY:

250980

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

13100

American (AMR)

AF:

0.00

AC:

AN:

13992

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

9288

East Asian (EAS)

AF:

0.00

AC:

AN:

24428

South Asian (SAS)

AF:

0.00432

AC:

203

AN:

46994

European-Finnish (FIN)

AF:

0.00

AC:

AN:

20900

Middle Eastern (MID)

AF:

0.00

AC:

AN:

1646

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

341532

Other (OTH)

AF:

0.000413

AC:

AN:

21768

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.485

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:

0.0000911

AC:

AN:

43892

Hom.:

Cov.:

AF XY:

0.0000922

AC XY:

AN XY:

21688

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

13364

American (AMR)

AF:

0.00

AC:

AN:

3632

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

1034

East Asian (EAS)

AF:

0.00

AC:

AN:

2556

South Asian (SAS)

AF:

0.00253

AC:

AN:

1580

European-Finnish (FIN)

AF:

0.00

AC:

AN:

3496

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

17278

Other (OTH)

AF:

0.00

AC:

AN:

526

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.475

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:

0.000790

AC:

ClinVar

ClinVar submissions

Significance:Likely benign

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.12

BayesDel_addAF

Benign

-0.30

BayesDel_noAF

Benign

-0.67

CADD

Benign

(source)

DANN

Benign

0.96

DEOGEN2

Benign

0.025

Eigen

Benign

-0.62

Eigen_PC

Benign

-0.83

FATHMM_MKL

Benign

0.0047

LIST_S2

Benign

0.40

M_CAP

Benign

0.021

MetaRNN

Benign

0.0075

MetaSVM

Benign

-0.97

PhyloP100

0.029

PROVEAN

Uncertain

-3.3

REVEL

Benign

0.037

Sift

Benign

0.088

Sift4G

Uncertain

0.053

Vest4

0.14

MutPred

0.16

Gain of ubiquitination at K456 (P = 0.0212)

MVP

0.24

ClinPred

0.077

GERP RS

0.71

Varity_R

0.33

gMVP

0.079

Mutation Taster

=97/3

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

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over