9-94318676-C-T

Variant names:

• chr9-94318676-C-T
• rs766323644
• NM_017561.2:c.2060G>A

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_017561.2(NUTM2F):​c.2060G>A​(p.Ser687Asn) 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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 23)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: NUTM2F NM_017561.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.136

Genes affected

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

LOC105376154 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.06720635).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NUTM2F	NM_017561.2	c.2060G>A	p.Ser687Asn	missense_variant	Exon 7 of 7	ENST00000253262.9	NP_060031.1
LOC105376154	XR_001746842.3	n.607+3666C>T		intron_variant	Intron 2 of 2
LOC105376154	XR_930132.4	n.190+3666C>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NUTM2F	ENST00000253262.9	c.2060G>A	p.Ser687Asn	missense_variant	Exon 7 of 7	1	NM_017561.2	ENSP00000253262.4

Frequencies

GnomAD3 genomes Cov.: 23

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 1443086 Hom.: 0 Cov.: 37 AF XY: 0.00 AC XY: 0 AN XY: 716318

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 23

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.20
BayesDel_addAF	Benign	-0.42	T
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.6
DANN	Benign	0.65
DEOGEN2	Benign	0.067	T;.
Eigen	Benign	-1.3
Eigen_PC	Benign	-1.4
FATHMM_MKL	Benign	0.0068	N
LIST_S2	Benign	0.41	T;T
M_CAP	Benign	0.0012	T
MetaRNN	Benign	0.067	T;T
MetaSVM	Benign	-0.96	T
MutationAssessor	Benign	1.8	L;.
PrimateAI	Benign	0.46	T
PROVEAN	Benign	-0.97	N;N
REVEL	Benign	0.015
Sift	Benign	0.23	T;T
Sift4G	Benign	0.17	T;T
Polyphen		0.0040	B;.
Vest4		0.093
MutPred		0.23		Loss of phosphorylation at S687 (P = 5e-04);.;
MVP		0.014
ClinPred		0.042	T
GERP RS		-0.49
Varity_R		0.074
gMVP		0.052

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

Other links and lift over

dbSNP: rs766323644; hg19: chr9-97080958;