15-34343662-G-T

Variant names:

• chr15-34343662-G-T
• rs73376010
• NM_001284292.2:c.-35G>T

Variant summary

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

The NM_001284293.2(NUTM1):​c.30G>T​(p.Lys10Asn) 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. 12/14 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: 32)
• Consequence: NUTM1 NM_001284293.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.134

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 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=0.05385843).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NUTM1	NM_001284292.2	c.-35G>T		5_prime_UTR_variant	Exon 1 of 8	ENST00000537011.6	NP_001271221.2
NUTM1	NM_001284293.2	c.30G>T	p.Lys10Asn	missense_variant	Exon 1 of 7		NP_001271222.2
NUTM1	NM_175741.3	c.-204G>T		5_prime_UTR_variant	Exon 1 of 8		NP_786883.2
NUTM1	XM_047432341.1	c.-207G>T		5_prime_UTR_variant	Exon 1 of 8		XP_047288297.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NUTM1	ENST00000537011	c.-35G>T		5_prime_UTR_variant	Exon 1 of 8	2	NM_001284292.2	ENSP00000444896.1
NUTM1	ENST00000333756	c.-204G>T		5_prime_UTR_variant	Exon 1 of 8	1		ENSP00000329448.4
NUTM1	ENST00000438749.7	c.30G>T	p.Lys10Asn	missense_variant	Exon 1 of 7	2		ENSP00000407031.3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 29

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Benign	-0.35	T
BayesDel_noAF	Benign	-0.73
CADD	Benign	8.1
DANN	Benign	0.47
Eigen	Benign	-0.86
Eigen_PC	Benign	-0.78
FATHMM_MKL	Benign	0.56	D
LIST_S2	Benign	0.25	T
M_CAP	Benign	0.0066	T
MetaRNN	Benign	0.054	T
MetaSVM	Benign	-0.96	T
PROVEAN	Benign	0.090	N
REVEL	Benign	0.030
Sift	Benign	1.0	T
Sift4G	Benign	0.71	T
Vest4		0.065
MutPred		0.15		Loss of MoRF binding (P = 0.0167);
MVP		0.12
ClinPred		0.080	T
GERP RS		2.1

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: rs73376010; hg19: chr15-34635863;