rs760672574

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr15-34348559-C-A
• chr15-34348559-C-G
• chr15-34348559-C-T

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>A​(p.Arg231Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,622 control chromosomes in the GnomAD database, with no homozygous occurrence. 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)
  • Exomes 𝑓: 6.8e-7 (0 hom.)
• 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=0.11932862).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NUTM1	NM_001284292.2	c.691C>A	p.Arg231Ser	missense_variant	Exon 3 of 8	ENST00000537011.6	NP_001271221.2
NUTM1	NM_001284293.2	c.661C>A	p.Arg221Ser	missense_variant	Exon 2 of 7		NP_001271222.2
NUTM1	NM_175741.3	c.607C>A	p.Arg203Ser	missense_variant	Exon 3 of 8		NP_786883.2
NUTM1	XM_047432341.1	c.607C>A	p.Arg203Ser	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>A	p.Arg231Ser	missense_variant	Exon 3 of 8	2	NM_001284292.2	ENSP00000444896.1
NUTM1	ENST00000333756.5	c.607C>A	p.Arg203Ser	missense_variant	Exon 3 of 8	1		ENSP00000329448.4
NUTM1	ENST00000438749.7	c.661C>A	p.Arg221Ser	missense_variant	Exon 2 of 7	2		ENSP00000407031.3

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 6.84e-7 AC: 1 AN: 1461622 Hom.: 0 Cov.: 36 AF XY: 0.00000138 AC XY: 1 AN XY: 727084

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: 8.99e-7

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.14
BayesDel_addAF	Benign	-0.22	T
BayesDel_noAF	Benign	-0.55
CADD	Benign	10
DANN	Benign	0.60
DEOGEN2	Benign	0.00015	.;T;.;T
Eigen	Benign	-0.18
Eigen_PC	Benign	-0.10
FATHMM_MKL	Uncertain	0.84	D
LIST_S2	Benign	0.35	T;T;T;.
M_CAP	Benign	0.0063	T
MetaRNN	Benign	0.12	T;T;T;T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	0.0	.;N;.;N
PrimateAI	Benign	0.30	T
PROVEAN	Benign	0.90	N;.;N;N
REVEL	Benign	0.034
Sift	Benign	0.48	T;.;T;T
Sift4G	Benign	0.85	T;T;T;T
Polyphen		0.18	.;B;.;B
Vest4		0.16
MutPred		0.31		.;Loss of catalytic residue at R203 (P = 0.0169);.;Loss of catalytic residue at R203 (P = 0.0169);
MVP		0.38
MPC		0.084
ClinPred		0.34	T
GERP RS		5.4
Varity_R		0.071
gMVP		0.15

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr15-34640760;