Variant 15-34348137-T-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_001284292.2(NUTM1):c.269T>A(p.Met90Lys) variant causes a missense change. The variant allele was found at a frequency of 0.000000684 in 1,461,892 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 32)

Exomes 𝑓: 6.8e-7 ( 0 hom. )

Consequence

NUTM1
NM_001284292.2 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 3.92

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:

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (MetaRNN=0.24574167).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
NUTM1	NM_001284292.2 linkuse as main transcript	c.269T>A	p.Met90Lys	missense_variant	3/8	ENST00000537011.6	NP_001271221.2
NUTM1	NM_001284293.2 linkuse as main transcript	c.239T>A	p.Met80Lys	missense_variant	2/7		NP_001271222.2
NUTM1	NM_175741.3 linkuse as main transcript	c.185T>A	p.Met62Lys	missense_variant	3/8		NP_786883.2
NUTM1	XM_047432341.1 linkuse as main transcript	c.185T>A	p.Met62Lys	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.269T>A	p.Met90Lys	missense_variant	3/8	2	NM_001284292.2	ENSP00000444896	A2	Q86Y26-4
NUTM1	ENST00000333756.5 linkuse as main transcript	c.185T>A	p.Met62Lys	missense_variant	3/8	1		ENSP00000329448	P2	Q86Y26-1
NUTM1	ENST00000438749.7 linkuse as main transcript	c.239T>A	p.Met80Lys	missense_variant	2/7	2		ENSP00000407031	A2	Q86Y26-3

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

6.84e-7

AC:

AN:

1461892

Hom.:

Cov.:

AF XY:

0.00000138

AC XY:

AN XY:

727246

show subpopulations

Gnomad4 AFR exome

AF:

0.0000299

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:

0.00

GnomAD4 genome

Cov.:

Bravo

AF:

0.00000756

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 14, 2024

The c.185T>A (p.M62K) alteration is located in exon 2 (coding exon 2) of the NUTM1 gene. This alteration results from a T to A substitution at nucleotide position 185, causing the methionine (M) at amino acid position 62 to be replaced by a lysine (K). 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

0.18

BayesDel_addAF

Benign

-0.15

BayesDel_noAF

Benign

-0.45

CADD

Benign

DANN

Benign

0.97

DEOGEN2

Benign

0.0088

.;T;.;T

Eigen

Benign

0.11

Eigen_PC

Uncertain

0.26

FATHMM_MKL

Uncertain

0.87

LIST_S2

Benign

0.44

T;T;T;.

M_CAP

Benign

0.0073

MetaRNN

Benign

0.25

T;T;T;T

MetaSVM

Benign

-1.0

MutationAssessor

Benign

0.69

.;N;.;N

MutationTaster

Benign

0.99

N;N;N

PrimateAI

Benign

0.37

PROVEAN

Benign

-2.4

N;.;N;N

REVEL

Benign

0.052

Sift

Uncertain

0.0030

D;.;D;D

Sift4G

Uncertain

0.016

D;D;D;D

Polyphen

0.47

.;P;.;P

Vest4

0.39

MutPred

0.32

.;Gain of ubiquitination at M62 (P = 0.0085);.;Gain of ubiquitination at M62 (P = 0.0085);

MVP

0.46

MPC

0.24

ClinPred

0.70

GERP RS

5.7

Varity_R

0.63

gMVP

0.35

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

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