NM_001355263.2:c.1126C>G

Variant names:

• chr10-79846873-C-G
• rs1842024251
• NM_001355263.2:c.1126C>G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 0P and 2B. BP4_Moderate

The NM_001355263.2(NUTM2E):​c.1126C>G​(p.Leu376Val) 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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. L376L) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 16)
• Consequence: NUTM2E NM_001355263.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.522
• Publications: 0 publications found

Genes affected

NUTM2E (HGNC:23448): (NUT family member 2E)

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.15936899).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001355263.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NUTM2E	NM_001355263.2	MANE Select	c.1126C>G	p.Leu376Val	missense	Exon 6 of 10	NP_001342192.1	B1AL46

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NUTM2E	ENST00000429984.5	TSL:5 MANE Select	c.1126C>G	p.Leu376Val	missense	Exon 6 of 10	ENSP00000407521.2	B1AL46
	NUTM2E	ENST00000602967.5	TSL:5	c.1126C>G	p.Leu376Val	missense	Exon 3 of 6	ENSP00000473558.1	R4GNA6

Frequencies

GnomAD3 genomes Cov.: 16

GnomAD4 exome Cov.: 9

GnomAD4 genome Cov.: 16

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.11
BayesDel_addAF	Benign	-0.25	T
BayesDel_noAF	Benign	-0.60
CADD	Benign	19
DANN	Uncertain	0.99
DEOGEN2	Benign	0.033	T
Eigen	Benign	-0.30
Eigen_PC	Benign	-0.42
FATHMM_MKL	Benign	0.17	N
LIST_S2	Benign	0.81	T
M_CAP	Benign	0.016	T
MetaRNN	Benign	0.16	T
MetaSVM	Benign	-1.1	T
PhyloP100		0.52
PROVEAN	Benign	-1.8	N
REVEL	Benign	0.015
Sift	Benign	0.21	T
Sift4G	Benign	0.21	T
Vest4		0.16
MutPred		0.17		Gain of catalytic residue at L376 (P = 0.0231)
MVP		0.12
ClinPred		0.75	D
GERP RS		0.68
Varity_R		0.15
gMVP		0.029
Mutation Taster		=90/10	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1842024251; hg19: chr10-81606629;