10-87228352-G-A

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The NM_001099338.2(NUTM2A):​c.472G>A​(p.Gly158Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.00037 ( 1 hom., cov: 21)
Exomes 𝑓: 0.00053 ( 10 hom. )
Failed GnomAD Quality Control

Consequence

NUTM2A
NM_001099338.2 missense

Scores

1
17

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: -0.104
Variant links:
Genes affected
NUTM2A (HGNC:23438): (NUT family member 2A)
NUTM2A-AS1 (HGNC:45161): (NUTM2A antisense RNA 1)

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.019382864).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
NUTM2ANM_001099338.2 linkc.472G>A p.Gly158Ser missense_variant Exon 2 of 7 ENST00000381707.6 NP_001092808.1 Q8IVF1-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
NUTM2AENST00000381707.6 linkc.472G>A p.Gly158Ser missense_variant Exon 2 of 7 1 NM_001099338.2 ENSP00000371126.1 Q8IVF1-1

Frequencies

GnomAD3 genomes
AF:
0.000368
AC:
56
AN:
152096
Hom.:
1
Cov.:
21
show subpopulations
Gnomad AFR
AF:
0.000169
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000262
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000208
Gnomad FIN
AF:
0.0000942
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000633
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.000359
AC:
83
AN:
231424
Hom.:
0
AF XY:
0.000315
AC XY:
40
AN XY:
127028
show subpopulations
Gnomad AFR exome
AF:
0.000155
Gnomad AMR exome
AF:
0.000684
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.0000571
Gnomad SAS exome
AF:
0.0000682
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000468
Gnomad OTH exome
AF:
0.00124
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
0.000531
AC:
775
AN:
1458518
Hom.:
10
Cov.:
32
AF XY:
0.000518
AC XY:
376
AN XY:
725568
show subpopulations
Gnomad4 AFR exome
AF:
0.000120
Gnomad4 AMR exome
AF:
0.000739
Gnomad4 ASJ exome
AF:
0.0000766
Gnomad4 EAS exome
AF:
0.0000252
Gnomad4 SAS exome
AF:
0.0000581
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.000630
Gnomad4 OTH exome
AF:
0.000465
GnomAD4 genome
Data not reliable, filtered out with message: AS_VQSR
AF:
0.000368
AC:
56
AN:
152212
Hom.:
1
Cov.:
21
AF XY:
0.000363
AC XY:
27
AN XY:
74432
show subpopulations
Gnomad4 AFR
AF:
0.000168
Gnomad4 AMR
AF:
0.000261
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000208
Gnomad4 FIN
AF:
0.0000942
Gnomad4 NFE
AF:
0.000633
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.000288
Hom.:
0
ExAC
AF:
0.000256
AC:
30

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
Jul 13, 2021
Ambry Genetics
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The c.472G>A (p.G158S) alteration is located in exon 2 (coding exon 2) of the NUTM2A gene. This alteration results from a G to A substitution at nucleotide position 472, causing the glycine (G) at amino acid position 158 to be replaced by a serine (S). 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
0.087
BayesDel_addAF
Benign
-0.54
T
BayesDel_noAF
Benign
-0.65
CADD
Benign
4.6
DANN
Benign
0.87
DEOGEN2
Benign
0.0094
T;.
Eigen
Benign
-1.1
Eigen_PC
Benign
-1.3
FATHMM_MKL
Benign
0.0020
N
LIST_S2
Benign
0.54
T;T
M_CAP
Benign
0.0011
T
MetaRNN
Benign
0.019
T;T
MetaSVM
Benign
-1.0
T
PrimateAI
Uncertain
0.56
T
PROVEAN
Benign
-2.0
N;N
REVEL
Benign
0.014
Sift
Benign
0.16
T;T
Sift4G
Benign
0.24
T;T
Polyphen
0.050
B;.
Vest4
0.11
MVP
0.043
ClinPred
0.0033
T
GERP RS
0.33
Varity_R
0.047
gMVP
0.15

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.

Other links and lift over

dbSNP: rs533509950; hg19: chr10-88988109; COSMIC: COSV67742022; API