GeneBe

rs764458811

Variant names:

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

4
14

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]

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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

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
NUTM1
NM_001284292.2
MANE Select
c.739C>Ap.Arg247Ser
missense
Exon 3 of 8NP_001271221.2Q86Y26-4
NUTM1
NM_001284293.2
c.709C>Ap.Arg237Ser
missense
Exon 2 of 7NP_001271222.2Q86Y26-3
NUTM1
NM_175741.3
c.655C>Ap.Arg219Ser
missense
Exon 3 of 8NP_786883.2Q86Y26-1

Ensembl Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
NUTM1
ENST00000537011.6
TSL:2 MANE Select
c.739C>Ap.Arg247Ser
missense
Exon 3 of 8ENSP00000444896.1Q86Y26-4
NUTM1
ENST00000333756.5
TSL:1
c.655C>Ap.Arg219Ser
missense
Exon 3 of 8ENSP00000329448.4Q86Y26-1
NUTM1
ENST00000438749.7
TSL:2
c.709C>Ap.Arg237Ser
missense
Exon 2 of 7ENSP00000407031.3Q86Y26-3

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
1458986
Hom.:
0
Cov.:
36
AF XY:
0.00
AC XY:
0
AN XY:
725950
African (AFR)
AF:
0.00
AC:
0
AN:
33476
American (AMR)
AF:
0.00
AC:
0
AN:
44722
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
26136
East Asian (EAS)
AF:
0.00
AC:
0
AN:
39700
South Asian (SAS)
AF:
0.00
AC:
0
AN:
86258
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
50582
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
5766
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
1111970
Other (OTH)
AF:
0.00
AC:
0
AN:
60376
GnomAD4 genome
Cov.:
33

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
T
BayesDel_noAF
Benign
-0.31
CADD
Benign
15
DANN
Uncertain
0.99
DEOGEN2
Benign
0.039
T
Eigen
Benign
0.14
Eigen_PC
Benign
0.14
FATHMM_MKL
Benign
0.71
D
LIST_S2
Benign
0.70
T
M_CAP
Benign
0.030
D
MetaRNN
Benign
0.37
T
MetaSVM
Benign
-0.72
T
MutationAssessor
Uncertain
2.7
M
PhyloP100
0.58
PrimateAI
Benign
0.23
T
PROVEAN
Uncertain
-3.0
D
REVEL
Benign
0.14
Sift
Benign
0.071
T
Sift4G
Uncertain
0.0090
D
Polyphen
0.98
D
Vest4
0.53
MutPred
0.36
Loss of MoRF binding (P = 0.0426)
MVP
0.35
MPC
0.23
ClinPred
0.95
D
GERP RS
3.8
Varity_R
0.24
gMVP
0.18
Mutation Taster
=88/12
polymorphism

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

Other links and lift over

dbSNP: rs764458811; hg19: chr15-34640808; API