15-34348559-C-G

Variant names:

• chr15-34348559-C-G
• rs760672574
• NM_001284292.2:c.691C>G

Variant summary

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

The NM_001284292.2(NUTM1):​c.691C>G​(p.Arg231Gly) 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. 15/21 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. R231C) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 33)
• Consequence: NUTM1 NM_001284292.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.70

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]

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=0.14045367).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NUTM1	NM_001284292.2	c.691C>G	p.Arg231Gly	missense_variant	Exon 3 of 8	ENST00000537011.6	NP_001271221.2
NUTM1	NM_001284293.2	c.661C>G	p.Arg221Gly	missense_variant	Exon 2 of 7		NP_001271222.2
NUTM1	NM_175741.3	c.607C>G	p.Arg203Gly	missense_variant	Exon 3 of 8		NP_786883.2
NUTM1	XM_047432341.1	c.607C>G	p.Arg203Gly	missense_variant	Exon 3 of 8		XP_047288297.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NUTM1	ENST00000537011.6	c.691C>G	p.Arg231Gly	missense_variant	Exon 3 of 8	2	NM_001284292.2	ENSP00000444896.1
NUTM1	ENST00000333756.5	c.607C>G	p.Arg203Gly	missense_variant	Exon 3 of 8	1		ENSP00000329448.4
NUTM1	ENST00000438749.7	c.661C>G	p.Arg221Gly	missense_variant	Exon 2 of 7	2		ENSP00000407031.3

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 36

GnomAD4 genome Cov.: 33

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.080
BayesDel_addAF	Benign	-0.21	T
BayesDel_noAF	Benign	-0.54
CADD	Benign	13
DANN	Benign	0.93
DEOGEN2	Benign	0.0012	.;T;.;T
Eigen	Benign	-0.044
Eigen_PC	Benign	-0.00058
FATHMM_MKL	Uncertain	0.91	D
LIST_S2	Benign	0.53	T;T;T;.
M_CAP	Benign	0.0067	T
MetaRNN	Benign	0.14	T;T;T;T
MetaSVM	Benign	-1.1	T
MutationAssessor	Benign	0.69	.;N;.;N
PrimateAI	Benign	0.29	T
PROVEAN	Benign	-0.77	N;.;N;N
REVEL	Benign	0.043
Sift	Benign	0.33	T;.;T;T
Sift4G	Benign	0.36	T;T;T;T
Polyphen		0.51	.;P;.;P
Vest4		0.14
MutPred		0.26		.;Gain of relative solvent accessibility (P = 0.0275);.;Gain of relative solvent accessibility (P = 0.0275);
MVP		0.36
MPC		0.14
ClinPred		0.50	D
GERP RS		5.4
Varity_R		0.10
gMVP		0.10

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: rs760672574; hg19: chr15-34640760;