NM_017561.2:c.1667C>T

Variant names:

• chr9-94319069-G-A
• NM_017561.2:c.1667C>T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_017561.2(NUTM2F):​c.1667C>T​(p.Ala556Val) 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. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 8)
• Consequence: NUTM2F NM_017561.2 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: -0.0930

Genes affected

NUTM2F (HGNC:23450): (NUT family member 2F)

LOC105376154 (HGNC:):

ACMG classification

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=0.09694058).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NUTM2F	NM_017561.2	c.1667C>T	p.Ala556Val	missense_variant	Exon 7 of 7	ENST00000253262.9	NP_060031.1
LOC105376154	XR_001746842.3	n.607+4059G>A		intron_variant	Intron 2 of 2
LOC105376154	XR_930132.4	n.190+4059G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NUTM2F	ENST00000253262.9	c.1667C>T	p.Ala556Val	missense_variant	Exon 7 of 7	1	NM_017561.2	ENSP00000253262.4

Frequencies

GnomAD3 genomes Cov.: 8

GnomAD4 exome Cov.: 29

GnomAD4 genome Cov.: 8

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Jun 06, 2023

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.1667C>T (p.A556V) alteration is located in exon 7 (coding exon 7) of the NUTM2F gene. This alteration results from a C to T substitution at nucleotide position 1667, causing the alanine (A) at amino acid position 556 to be replaced by a valine (V). 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	0.11
BayesDel_addAF	Benign	-0.30	T
BayesDel_noAF	Benign	-0.67
CADD	Benign	3.4
DANN	Benign	0.90
DEOGEN2	Benign	0.011	T;.
Eigen	Benign	-0.91
Eigen_PC	Benign	-1.1
FATHMM_MKL	Benign	0.0053	N
LIST_S2	Benign	0.70	T;T
M_CAP	Benign	0.0013	T
MetaRNN	Benign	0.097	T;T
MetaSVM	Benign	-0.99	T
MutationAssessor	Benign	2.0	M;.
PrimateAI	Benign	0.29	T
PROVEAN	Benign	-1.5	N;N
REVEL	Benign	0.023
Sift	Uncertain	0.017	D;D
Sift4G	Benign	0.45	T;T
Polyphen		0.16	B;.
Vest4		0.079
MutPred		0.16		Gain of sheet (P = 0.0266);.;
MVP		0.014
ClinPred		0.053	T
GERP RS		0.17
Varity_R		0.054
gMVP		0.058

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr9-97081351;