Variant chr10-79711875-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_StrongBP6

The NM_001278495.2(NUTM2B):c.2027T>C(p.Met676Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 13/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).

Frequency

Genomes: 𝑓 0.052 ( 494 hom., cov: 27)

Exomes 𝑓: 0.039 ( 21142 hom. )

Failed GnomAD Quality Control

Consequence

NUTM2B
NM_001278495.2 missense

Scores

Clinical Significance

Benign/Likely benign no assertion criteria provided B:2

Conservation

PhyloP100: -4.51

Variant links:

Genes affected

NUTM2B (HGNC:23445): (NUT family member 2B)

NUTM2B links:

NUTM2B-AS1 (HGNC:51204): (NUTM2B antisense RNA 1)

NUTM2B-AS1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -5 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.004448861).

BP6

Variant 10-79711875-T-C is Benign according to our data. Variant chr10-79711875-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 1206196.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-79711875-T-C is described in Lovd as [Benign]. Variant chr10-79711875-T-C is described in Lovd as [Likely_benign].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
NUTM2B	NM_001278495.2 linkuse as main transcript	c.2027T>C	p.Met676Thr	missense_variant	7/7	ENST00000429828.7
NUTM2B-AS1	NR_120613.1 linkuse as main transcript	n.757-19819A>G		intron_variant, non_coding_transcript_variant
NUTM2B	XM_047425707.1 linkuse as main transcript	c.2027T>C	p.Met676Thr	missense_variant	9/9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NUTM2B	ENST00000429828.7 linkuse as main transcript	c.2027T>C	p.Met676Thr	missense_variant	7/7	5	NM_001278495.2	P1	A6NNL0-1
NUTM2B-AS1	ENST00000671459.1 linkuse as main transcript	n.146-48641A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

5707

AN:

110256

Hom.:

491

Cov.:

FAILED QC

Gnomad AFR

AF:

0.0834

Gnomad AMI

AF:

0.00917

Gnomad AMR

AF:

0.0757

Gnomad ASJ

AF:

0.0856

Gnomad EAS

AF:

0.0123

Gnomad SAS

AF:

0.0543

Gnomad FIN

AF:

0.0237

Gnomad MID

AF:

0.0252

Gnomad NFE

AF:

0.0375

Gnomad OTH

AF:

0.0450

GnomAD3 exomes

AF:

0.0175

AC:

3797

AN:

216746

Hom.:

1866

AF XY:

0.0164

AC XY:

1923

AN XY:

117070

show subpopulations

Gnomad AFR exome

AF:

0.0102

Gnomad AMR exome

AF:

0.0405

Gnomad ASJ exome

AF:

0.00712

Gnomad EAS exome

AF:

0.0186

Gnomad SAS exome

AF:

0.0514

Gnomad FIN exome

AF:

0.00185

Gnomad NFE exome

AF:

0.00787

Gnomad OTH exome

AF:

0.0242

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.0387

AC:

50687

AN:

1309642

Hom.:

21142

Cov.:

AF XY:

0.0450

AC XY:

29196

AN XY:

648570

show subpopulations

Gnomad4 AFR exome

AF:

0.0342

Gnomad4 AMR exome

AF:

0.0876

Gnomad4 ASJ exome

AF:

0.0704

Gnomad4 EAS exome

AF:

0.0949

Gnomad4 SAS exome

AF:

0.212

Gnomad4 FIN exome

AF:

0.0795

Gnomad4 NFE exome

AF:

0.0211

Gnomad4 OTH exome

AF:

0.0483

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.0519

AC:

5724

AN:

110296

Hom.:

494

Cov.:

AF XY:

0.0525

AC XY:

2800

AN XY:

53298

show subpopulations

Gnomad4 AFR

AF:

0.0837

Gnomad4 AMR

AF:

0.0759

Gnomad4 ASJ

AF:

0.0856

Gnomad4 EAS

AF:

0.0123

Gnomad4 SAS

AF:

0.0552

Gnomad4 FIN

AF:

0.0237

Gnomad4 NFE

AF:

0.0375

Gnomad4 OTH

AF:

0.0453

Alfa

AF:

0.0919

Hom.:

620

ExAC

AF:

0.0000281

AC:

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:2

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, no assertion criteria provided

clinical testing

Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center

- -

not provided

Benign:1

Likely benign, no assertion criteria provided

clinical testing

Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC)

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.073

BayesDel_addAF

Benign

-0.43

BayesDel_noAF

Benign

-0.86

CADD

Benign

0.0010

DANN

Benign

0.17

DEOGEN2

Benign

0.00045

Eigen

Benign

-1.2

Eigen_PC

Benign

-1.4

FATHMM_MKL

Benign

0.00078

LIST_S2

Benign

0.22

M_CAP

Benign

0.0014

MetaRNN

Benign

0.0044

MetaSVM

Benign

-1.0

MutationTaster

Benign

1.0

N;N;N;N

PROVEAN

Benign

0.020

REVEL

Benign

0.0030

Sift

Benign

0.49

Sift4G

Benign

0.64

Vest4

0.039

ClinPred

0.0079

GERP RS

-2.1

Varity_R

0.037

gMVP

0.058

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

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