Genetic Variant NUTM2E:p.Pro538Pro (chr10-79848775-C-T) – ACMG Classification: Benign (-7 pts)

Variant summary

Our verdict is Benign. The variant received -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7

The NM_001355263.2(NUTM2E):c.1614C>T(p.Pro538Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0011 ( 5 hom., cov: 6)

Exomes 𝑓: 0.0017 ( 194 hom. )

Failed GnomAD Quality Control

Consequence

NUTM2E
NM_001355263.2 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.937

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: Benign. The variant received -7 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

BP6

Variant 10-79848775-C-T is Benign according to our data. Variant chr10-79848775-C-T is described in CliVar as Likely_benign. Clinvar id is 2640649.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr10-79848775-C-T is described in CliVar as Likely_benign. Clinvar id is 2640649.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr10-79848775-C-T is described in CliVar as Likely_benign. Clinvar id is 2640649.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-0.937 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NUTM2E	NM_001355263.2 link	c.1614C>T	p.Pro538Pro	synonymous_variant	Exon 8 of 10	ENST00000429984.5	NP_001342192.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NUTM2E	ENST00000429984.5 link	c.1614C>T	p.Pro538Pro	synonymous_variant	Exon 8 of 10	5	NM_001355263.2	ENSP00000407521.2		B1AL46
NUTM2E	ENST00000602967.5 link	c.1614C>T	p.Pro538Pro	synonymous_variant	Exon 5 of 6	5		ENSP00000473558.1		R4GNA6

Frequencies

GnomAD3 genomes

AF:

0.00108

AC:

AN:

58540

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000113

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00133

Gnomad ASJ

AF:

0.000663

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000473

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.0135

Gnomad NFE

AF:

0.00214

Gnomad OTH

AF:

0.00

GnomAD2 exomes

AF:

0.00128

AC:

AN:

56876

AF XY:

0.00134

show subpopulations

Gnomad AFR exome

AF:

0.000551

Gnomad AMR exome

AF:

0.000647

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.000121

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00307

Gnomad OTH exome

AF:

0.00342

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.00173

AC:

828

AN:

477936

Hom.:

194

Cov.:

AF XY:

0.00160

AC XY:

397

AN XY:

248886

show subpopulations

African (AFR)

AF:

0.000430

AC:

AN:

16262

American (AMR)

AF:

0.000900

AC:

AN:

19996

Ashkenazi Jewish (ASJ)

AF:

0.0000732

AC:

AN:

13662

East Asian (EAS)

AF:

0.0000364

AC:

AN:

27464

South Asian (SAS)

AF:

0.000804

AC:

AN:

51018

European-Finnish (FIN)

AF:

0.0000718

AC:

AN:

27848

Middle Eastern (MID)

AF:

0.000992

AC:

AN:

2016

European-Non Finnish (NFE)

AF:

0.00248

AC:

731

AN:

294872

Other (OTH)

AF:

0.00101

AC:

AN:

24798

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.481

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

100

<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:

0.00107

AC:

AN:

58658

Hom.:

Cov.:

AF XY:

0.000972

AC XY:

AN XY:

28798

show subpopulations

African (AFR)

AF:

0.000113

AC:

AN:

17770

American (AMR)

AF:

0.00133

AC:

AN:

6030

Ashkenazi Jewish (ASJ)

AF:

0.000663

AC:

AN:

1508

East Asian (EAS)

AF:

0.00

AC:

AN:

2792

South Asian (SAS)

AF:

0.000471

AC:

AN:

2122

European-Finnish (FIN)

AF:

0.00

AC:

AN:

4428

Middle Eastern (MID)

AF:

0.0156

AC:

AN:

128

European-Non Finnish (NFE)

AF:

0.00214

AC:

AN:

22868

Other (OTH)

AF:

0.00

AC:

AN:

736

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.468

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome 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

Alfa

AF:

0.00809

Hom.:

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Nov 01, 2022

CeGaT Center for Human Genetics Tuebingen

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

NUTM2E: BP4, BP7, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

4.1

(source)

DANN

Benign

0.59

PhyloP100

-0.94

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over