Variant chr15-34343662-G-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_001284292.2(NUTM1):c.-35G>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.149 in 1,533,972 control chromosomes in the GnomAD database, including 18,178 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.15 ( 1795 hom., cov: 32)

Exomes 𝑓: 0.15 ( 16383 hom. )

Consequence

NUTM1
NM_001284292.2 5_prime_UTR

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.134

Variant links:

Genes affected

NUTM1 (HGNC:29919): (NUT midline carcinoma family member 1) Predicted to be located in cytoplasm and nucleus. [provided by Alliance of Genome Resources, Apr 2022]

NUTM1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0044864714).

BP6

Variant 15-34343662-G-C is Benign according to our data. Variant chr15-34343662-G-C is described in ClinVar as [Benign]. Clinvar id is 403246.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.316 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
NUTM1	NM_001284292.2 linkuse as main transcript	c.-35G>C		5_prime_UTR_variant	1/8	ENST00000537011.6
NUTM1	NM_001284293.2 linkuse as main transcript	c.30G>C	p.Lys10Asn	missense_variant	1/7
NUTM1	NM_175741.3 linkuse as main transcript	c.-204G>C		5_prime_UTR_variant	1/8
NUTM1	XM_047432341.1 linkuse as main transcript	c.-207G>C		5_prime_UTR_variant	1/8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NUTM1	ENST00000537011.6 linkuse as main transcript	c.-35G>C		5_prime_UTR_variant	1/8	2	NM_001284292.2	A2	Q86Y26-4
NUTM1	ENST00000333756.5 linkuse as main transcript	c.-204G>C		5_prime_UTR_variant	1/8	1		P2	Q86Y26-1
NUTM1	ENST00000438749.7 linkuse as main transcript	c.30G>C	p.Lys10Asn	missense_variant	1/7	2		A2	Q86Y26-3

Frequencies

GnomAD3 genomes

AF:

0.150

AC:

22775

AN:

152102

Hom.:

1793

Cov.:

show subpopulations

Gnomad AFR

AF:

0.144

Gnomad AMI

AF:

0.235

Gnomad AMR

AF:

0.161

Gnomad ASJ

AF:

0.118

Gnomad EAS

AF:

0.329

Gnomad SAS

AF:

0.204

Gnomad FIN

AF:

0.104

Gnomad MID

AF:

0.149

Gnomad NFE

AF:

0.141

Gnomad OTH

AF:

0.148

GnomAD3 exomes

AF:

0.168

AC:

21590

AN:

128342

Hom.:

2039

AF XY:

0.170

AC XY:

11926

AN XY:

70300

show subpopulations

Gnomad AFR exome

AF:

0.153

Gnomad AMR exome

AF:

0.158

Gnomad ASJ exome

AF:

0.125

Gnomad EAS exome

AF:

0.319

Gnomad SAS exome

AF:

0.202

Gnomad FIN exome

AF:

0.110

Gnomad NFE exome

AF:

0.141

Gnomad OTH exome

AF:

0.165

GnomAD4 exome

AF:

0.149

AC:

206075

AN:

1381752

Hom.:

16383

Cov.:

AF XY:

0.151

AC XY:

102664

AN XY:

681866

show subpopulations

Gnomad4 AFR exome

AF:

0.150

Gnomad4 AMR exome

AF:

0.161

Gnomad4 ASJ exome

AF:

0.127

Gnomad4 EAS exome

AF:

0.302

Gnomad4 SAS exome

AF:

0.202

Gnomad4 FIN exome

AF:

0.115

Gnomad4 NFE exome

AF:

0.141

Gnomad4 OTH exome

AF:

0.148

GnomAD4 genome

AF:

0.150

AC:

22788

AN:

152220

Hom.:

1795

Cov.:

AF XY:

0.153

AC XY:

11424

AN XY:

74434

show subpopulations

Gnomad4 AFR

AF:

0.144

Gnomad4 AMR

AF:

0.162

Gnomad4 ASJ

AF:

0.118

Gnomad4 EAS

AF:

0.329

Gnomad4 SAS

AF:

0.203

Gnomad4 FIN

AF:

0.104

Gnomad4 NFE

AF:

0.141

Gnomad4 OTH

AF:

0.148

Alfa

AF:

0.139

Hom.:

267

Bravo

AF:

0.154

TwinsUK

AF:

0.135

AC:

502

ALSPAC

AF:

0.148

AC:

572

ExAC

AF:

0.157

AC:

2147

Asia WGS

AF:

0.222

AC:

772

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Mar 29, 2016

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: MAF -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.77

BayesDel_noAF

Benign

-0.74

CADD

Benign

7.7

DANN

Benign

0.50

Eigen

Benign

-0.86

Eigen_PC

Benign

-0.78

FATHMM_MKL

Benign

0.16

LIST_S2

Benign

0.25

MetaRNN

Benign

0.0045

MetaSVM

Benign

-0.91

MutationTaster

Benign

1.0

P;P

PROVEAN

Benign

0.090

REVEL

Benign

0.023

Sift

Benign

1.0

Sift4G

Benign

0.71

Vest4

0.065

MutPred

0.15

Loss of MoRF binding (P = 0.0167);

ClinPred

0.0035

GERP RS

2.1

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