rs442873

Positions:

• chr15-34352442-G-A
• chr15-34352442-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001284292.2(NUTM1):​c.939-1294G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.89 in 151,958 control chromosomes in the GnomAD database, including 60,551 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.89 (60551 hom., cov: 29)
• Consequence: NUTM1 NM_001284292.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.420

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 Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.935 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NUTM1	NM_001284292.2	c.939-1294G>A		intron_variant		ENST00000537011.6	NP_001271221.2
NUTM1	NM_001284293.2	c.909-1294G>A		intron_variant			NP_001271222.2
NUTM1	NM_175741.3	c.855-1294G>A		intron_variant			NP_786883.2
NUTM1	XM_047432341.1	c.855-1294G>A		intron_variant			XP_047288297.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NUTM1	ENST00000537011.6	c.939-1294G>A		intron_variant		2	NM_001284292.2	ENSP00000444896	A2
NUTM1	ENST00000333756.5	c.855-1294G>A		intron_variant		1		ENSP00000329448	P2
NUTM1	ENST00000438749.7	c.909-1294G>A		intron_variant		2		ENSP00000407031	A2

Frequencies

GnomAD3 genomes AF: 0.890 AC: 135186 AN: 151840 Hom.: 60513 Cov.: 29

Gnomad AFR AF: 0.809

Gnomad AMI AF: 0.891

Gnomad AMR AF: 0.868

Gnomad ASJ AF: 0.925

Gnomad EAS AF: 0.793

Gnomad SAS AF: 0.879

Gnomad FIN AF: 0.949

Gnomad MID AF: 0.936

Gnomad NFE AF: 0.941

Gnomad OTH AF: 0.904

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.890 AC: 135277 AN: 151958 Hom.: 60551 Cov.: 29 AF XY: 0.891 AC XY: 66157 AN XY: 74286

Gnomad4 AFR AF: 0.809

Gnomad4 AMR AF: 0.867

Gnomad4 ASJ AF: 0.925

Gnomad4 EAS AF: 0.793

Gnomad4 SAS AF: 0.880

Gnomad4 FIN AF: 0.949

Gnomad4 NFE AF: 0.941

Gnomad4 OTH AF: 0.902

Alfa AF: 0.933 Hom.: 93550

Bravo AF: 0.879

Asia WGS AF: 0.851 AC: 2961 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.69
DANN	Benign	0.47

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: rs442873; hg19: chr15-34644643;