Variant 10-79710644-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1

The NM_001278495.2(NUTM2B):c.1614C>T(p.Pro538=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0549 in 113,816 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.055 ( 4 hom., cov: 24)

Exomes 𝑓: 0.19 ( 343 hom. )

Failed GnomAD Quality Control

Consequence

NUTM2B
NM_001278495.2 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.435

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 Benign. Variant got -15 ACMG points.

BP4

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

BP6

Variant 10-79710644-C-T is Benign according to our data. Variant chr10-79710644-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 771885.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-0.435 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0876 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
NUTM2B	NM_001278495.2 linkuse as main transcript	c.1614C>T	p.Pro538=	synonymous_variant	5/7	ENST00000429828.7
NUTM2B-AS1	NR_120613.1 linkuse as main transcript	n.757-18588G>A		intron_variant, non_coding_transcript_variant
NUTM2B	XM_047425707.1 linkuse as main transcript	c.1614C>T	p.Pro538=	synonymous_variant	7/9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NUTM2B	ENST00000429828.7 linkuse as main transcript	c.1614C>T	p.Pro538=	synonymous_variant	5/7	5	NM_001278495.2	P1	A6NNL0-1
NUTM2B-AS1	ENST00000671459.1 linkuse as main transcript	n.146-47410G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.0549

AC:

6246

AN:

113694

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0176

Gnomad AMI

AF:

0.0318

Gnomad AMR

AF:

0.0457

Gnomad ASJ

AF:

0.104

Gnomad EAS

AF:

0.0244

Gnomad SAS

AF:

0.0960

Gnomad FIN

AF:

0.0394

Gnomad MID

AF:

0.0702

Gnomad NFE

AF:

0.0839

Gnomad OTH

AF:

0.0587

GnomAD3 exomes

AF:

0.00147

AC:

AN:

51666

Hom.:

AF XY:

0.00177

AC XY:

AN XY:

26030

show subpopulations

Gnomad AFR exome

AF:

0.00140

Gnomad AMR exome

AF:

0.000311

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.000334

Gnomad SAS exome

AF:

0.000639

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00283

Gnomad OTH exome

AF:

0.00114

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.187

AC:

216501

AN:

1155930

Hom.:

343

Cov.:

AF XY:

0.186

AC XY:

106299

AN XY:

571888

show subpopulations

Gnomad4 AFR exome

AF:

0.0417

Gnomad4 AMR exome

AF:

0.0790

Gnomad4 ASJ exome

AF:

0.172

Gnomad4 EAS exome

AF:

0.0358

Gnomad4 SAS exome

AF:

0.161

Gnomad4 FIN exome

AF:

0.0945

Gnomad4 NFE exome

AF:

0.210

Gnomad4 OTH exome

AF:

0.156

GnomAD4 genome

AF:

0.0549

AC:

6244

AN:

113816

Hom.:

Cov.:

AF XY:

0.0558

AC XY:

3113

AN XY:

55746

show subpopulations

Gnomad4 AFR

AF:

0.0176

Gnomad4 AMR

AF:

0.0457

Gnomad4 ASJ

AF:

0.104

Gnomad4 EAS

AF:

0.0244

Gnomad4 SAS

AF:

0.0963

Gnomad4 FIN

AF:

0.0394

Gnomad4 NFE

AF:

0.0838

Gnomad4 OTH

AF:

0.0583

Alfa

AF:

0.0368

Hom.:

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Invitae

Dec 31, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

3.8

DANN

Benign

0.64

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