Variant chr15-34348580-G-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001284292.2(NUTM1):c.712G>T(p.Val238Phe) variant causes a missense change. The variant allele was found at a frequency of 0.00000248 in 1,613,326 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.0000066 ( 0 hom., cov: 33)

Exomes 𝑓: 0.0000021 ( 0 hom. )

Consequence

NUTM1
NM_001284292.2 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 5.51

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 Uncertain_significance. Variant got 2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
NUTM1	NM_001284292.2 linkuse as main transcript	c.712G>T	p.Val238Phe	missense_variant	3/8	ENST00000537011.6	NP_001271221.2
NUTM1	NM_001284293.2 linkuse as main transcript	c.682G>T	p.Val228Phe	missense_variant	2/7		NP_001271222.2
NUTM1	NM_175741.3 linkuse as main transcript	c.628G>T	p.Val210Phe	missense_variant	3/8		NP_786883.2
NUTM1	XM_047432341.1 linkuse as main transcript	c.628G>T	p.Val210Phe	missense_variant	3/8		XP_047288297.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NUTM1	ENST00000537011.6 linkuse as main transcript	c.712G>T	p.Val238Phe	missense_variant	3/8	2	NM_001284292.2	ENSP00000444896	A2	Q86Y26-4
NUTM1	ENST00000333756.5 linkuse as main transcript	c.628G>T	p.Val210Phe	missense_variant	3/8	1		ENSP00000329448	P2	Q86Y26-1
NUTM1	ENST00000438749.7 linkuse as main transcript	c.682G>T	p.Val228Phe	missense_variant	2/7	2		ENSP00000407031	A2	Q86Y26-3

Frequencies

GnomAD3 genomes

AF:

0.00000657

AC:

AN:

152214

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000241

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00

Gnomad OTH

AF:

0.00

GnomAD4 exome

AF:

0.00000205

AC:

AN:

1461112

Hom.:

Cov.:

AF XY:

0.00000138

AC XY:

AN XY:

726860

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.00

Gnomad4 OTH exome

AF:

0.0000497

GnomAD4 genome

AF:

0.00000657

AC:

AN:

152214

Hom.:

Cov.:

AF XY:

0.0000134

AC XY:

AN XY:

74368

show subpopulations

Gnomad4 AFR

AF:

0.0000241

Gnomad4 AMR

AF:

0.00

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.00

Gnomad4 OTH

AF:

0.00

Bravo

AF:

0.0000189

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Feb 28, 2024

The c.628G>T (p.V210F) alteration is located in exon 2 (coding exon 2) of the NUTM1 gene. This alteration results from a G to T substitution at nucleotide position 628, causing the valine (V) at amino acid position 210 to be replaced by a phenylalanine (F). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.28

BayesDel_addAF

Pathogenic

0.25

BayesDel_noAF

Uncertain

0.13

CADD

Uncertain

DANN

Uncertain

1.0

DEOGEN2

Benign

0.094

.;T;.;T

Eigen

Pathogenic

0.80

Eigen_PC

Pathogenic

0.75

FATHMM_MKL

Uncertain

0.92

LIST_S2

Uncertain

0.90

D;D;D;.

M_CAP

Benign

0.031

MetaRNN

Uncertain

0.64

D;D;D;D

MetaSVM

Benign

-0.56

MutationAssessor

Pathogenic

3.2

.;M;.;M

MutationTaster

Benign

1.0

D;D;D

PrimateAI

Uncertain

0.56

PROVEAN

Pathogenic

-4.5

D;.;D;D

REVEL

Uncertain

0.31

Sift

Uncertain

0.021

D;.;D;D

Sift4G

Uncertain

0.023

D;D;D;D

Polyphen

1.0

.;D;.;D

Vest4

0.86

MutPred

0.35

.;Loss of ubiquitination at K205 (P = 0.0584);.;Loss of ubiquitination at K205 (P = 0.0584);

MVP

0.60

MPC

0.47

ClinPred

1.0

GERP RS

5.7

Varity_R

0.74

gMVP

0.50

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