NM_024617.4:c.4402C>A

Variant names:

• chr9-86301294-G-T
• NM_024617.4:c.4402C>A

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2 BP4

The NM_024617.4(TUT7):​c.4402C>A​(p.Gln1468Lys) variant causes a missense change. The variant allele was found at a frequency of 0.00000274 in 1,461,656 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0000027 (0 hom.)
• Consequence: TUT7 NM_024617.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.49

Genes affected

TUT7 (HGNC:25817): (terminal uridylyl transferase 7) Enables RNA uridylyltransferase activity and miRNA binding activity. Involved in RNA metabolic process and negative regulation of transposition, RNA-mediated. Located in cytosol and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Uncertain_significance. Variant got 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.2640673).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TUT7	NM_024617.4	c.4402C>A	p.Gln1468Lys	missense_variant	Exon 26 of 27	ENST00000375963.8	NP_078893.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TUT7	ENST00000375963.8	c.4402C>A	p.Gln1468Lys	missense_variant	Exon 26 of 27	5	NM_024617.4	ENSP00000365130.3
TUT7	ENST00000375960.6	c.3694C>A	p.Gln1232Lys	missense_variant	Exon 19 of 20	1		ENSP00000365127.2
TUT7	ENST00000277141.10	c.2269C>A	p.Gln757Lys	missense_variant	Exon 27 of 28	2		ENSP00000277141.6
TUT7	ENST00000375957.5	c.1102C>A	p.Gln368Lys	missense_variant	Exon 11 of 12	2		ENSP00000365124.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000274 AC: 4 AN: 1461656 Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2 AN XY: 727132

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: 0.00000360

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.17
BayesDel_addAF	Uncertain	0.12	D
BayesDel_noAF	Uncertain	-0.070
CADD	Pathogenic	26
DANN	Uncertain	0.99
DEOGEN2	Benign	0.038	.;.;T;T
Eigen	Uncertain	0.57
Eigen_PC	Uncertain	0.60
FATHMM_MKL	Uncertain	0.95	D
LIST_S2	Uncertain	0.95	D;D;D;D
M_CAP	Benign	0.034	D
MetaRNN	Benign	0.26	T;T;T;T
MetaSVM	Uncertain	0.12	D
MutationAssessor	Uncertain	2.2	.;.;.;M
PrimateAI	Uncertain	0.57	T
PROVEAN	Benign	-1.8	N;N;N;N
REVEL	Uncertain	0.36
Sift	Uncertain	0.0040	D;D;D;D
Sift4G	Uncertain	0.045	D;D;T;D
Polyphen		0.98, 0.99	.;D;.;D
Vest4		0.54
MutPred		0.35		.;.;.;Gain of methylation at Q1468 (P = 0.0034);
MVP		0.19
MPC		1.8
ClinPred		0.87	D
GERP RS		5.2
Varity_R		0.24
gMVP		0.32

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: chr9-88916209;