15-34343662-G-T

Variant names:

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

Variant summary

Our verdict is Likely benign. The variant received -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. 14/17 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 nucleotide change resulting in the same amino acid substitution has been previously reported as Benign in ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: NUTM1 NM_001284293.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.134
• Publications: 7 publications found

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

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

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.05385843).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001284293.2. 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
	NUTM1	NM_001284292.2	MANE Select	c.-35G>T		5_prime_UTR	Exon 1 of 8	NP_001271221.2	Q86Y26-4
	NUTM1	NM_001284293.2		c.30G>T	p.Lys10Asn	missense	Exon 1 of 7	NP_001271222.2	Q86Y26-3
	NUTM1	NM_175741.3		c.-204G>T		5_prime_UTR	Exon 1 of 8	NP_786883.2	Q86Y26-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NUTM1	ENST00000537011.6	TSL:2 MANE Select	c.-35G>T		5_prime_UTR	Exon 1 of 8	ENSP00000444896.1	Q86Y26-4
	NUTM1	ENST00000333756.5	TSL:1	c.-204G>T		5_prime_UTR	Exon 1 of 8	ENSP00000329448.4	Q86Y26-1
	NUTM1	ENST00000438749.7	TSL:2	c.30G>T	p.Lys10Asn	missense	Exon 1 of 7	ENSP00000407031.3	Q86Y26-3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 29

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.17
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
PhyloP100		-0.13
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
PromoterAI		-0.020	Neutral

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

Other links and lift over

dbSNP: rs73376010; hg19: chr15-34635863;