Genetic Variant NM_001284292.2:c.739C>A (chr15-34348607-C-A) – ACMG Classification: Uncertain_significance (1 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 1 ACMG points: 2P and 1B. PM2BP4

The NM_001284292.2(NUTM1):c.739C>A(p.Arg247Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 13/22 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R247H) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 33)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

NUTM1
NM_001284292.2 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.580

Publications

0 publications found

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 was made for transcript

Our verdict: Uncertain_significance. The variant received 1 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (MetaRNN=0.3707723).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001284292.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
NUTM1	NM_001284292.2	MANE Select	c.739C>A	p.Arg247Ser	missense	Exon 3 of 8	NP_001271221.2	Q86Y26-4
NUTM1	NM_001284293.2		c.709C>A	p.Arg237Ser	missense	Exon 2 of 7	NP_001271222.2	Q86Y26-3
NUTM1	NM_175741.3		c.655C>A	p.Arg219Ser	missense	Exon 3 of 8	NP_786883.2	Q86Y26-1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
NUTM1	ENST00000537011.6	TSL:2 MANE Select	c.739C>A	p.Arg247Ser	missense	Exon 3 of 8	ENSP00000444896.1	Q86Y26-4
NUTM1	ENST00000333756.5	TSL:1	c.655C>A	p.Arg219Ser	missense	Exon 3 of 8	ENSP00000329448.4	Q86Y26-1
NUTM1	ENST00000438749.7	TSL:2	c.709C>A	p.Arg237Ser	missense	Exon 2 of 7	ENSP00000407031.3	Q86Y26-3

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

1458986

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

725950

African (AFR)

AF:

0.00

AC:

AN:

33476

American (AMR)

AF:

0.00

AC:

AN:

44722

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

26136

East Asian (EAS)

AF:

0.00

AC:

AN:

39700

South Asian (SAS)

AF:

0.00

AC:

AN:

86258

European-Finnish (FIN)

AF:

0.00

AC:

AN:

50582

Middle Eastern (MID)

AF:

0.00

AC:

AN:

5766

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

1111970

Other (OTH)

AF:

0.00

AC:

AN:

60376

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.32

BayesDel_addAF

Benign

-0.051

BayesDel_noAF

Benign

-0.31

CADD

Benign

(source)

DANN

Uncertain

0.99

DEOGEN2

Benign

0.039

Eigen

Benign

0.14

Eigen_PC

Benign

0.14

FATHMM_MKL

Benign

0.71

LIST_S2

Benign

0.70

M_CAP

Benign

0.030

MetaRNN

Benign

0.37

MetaSVM

Benign

-0.72

MutationAssessor

Uncertain

2.7

PhyloP100

0.58

PrimateAI

Benign

0.23

PROVEAN

Uncertain

-3.0

REVEL

Benign

0.14

Sift

Benign

0.071

Sift4G

Uncertain

0.0090

Polyphen

0.98

Vest4

0.53

MutPred

0.36

Loss of MoRF binding (P = 0.0426)

MVP

0.35

MPC

0.23

ClinPred

0.95

GERP RS

3.8

Varity_R

0.24

gMVP

0.18

Mutation Taster

=88/12

polymorphism

(source)

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over