Genetic Variant TUT7:p.Ile1217Val (chr9-86309223-T-C) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_024617.4(TUT7):c.3649A>G(p.Ile1217Val) 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. 17/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 32)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

TUT7
NM_024617.4 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 1.78

Publications

2 publications found

Variant links:

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]

TUT7 links:

ENSG00000299358 (HGNC:):

ENSG00000299358 links:

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (MetaRNN=0.08841151).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024617.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
TUT7	NM_024617.4	MANE Select	c.3649A>G	p.Ile1217Val	missense	Exon 21 of 27	NP_078893.2
TUT7	NM_001185059.2		c.3649A>G	p.Ile1217Val	missense	Exon 21 of 27	NP_001171988.1	Q5VYS8-1
TUT7	NM_001185074.2		c.2941A>G	p.Ile981Val	missense	Exon 14 of 20	NP_001172003.1	Q5VYS8-4

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
TUT7	ENST00000375963.8	TSL:5 MANE Select	c.3649A>G	p.Ile1217Val	missense	Exon 21 of 27	ENSP00000365130.3	Q5VYS8-1
TUT7	ENST00000375960.6	TSL:1	c.2941A>G	p.Ile981Val	missense	Exon 14 of 20	ENSP00000365127.2	Q5VYS8-4
TUT7	ENST00000896499.1		c.3649A>G	p.Ile1217Val	missense	Exon 21 of 29	ENSP00000566558.1

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

1416978

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

706908

African (AFR)

AF:

0.00

AC:

AN:

32120

American (AMR)

AF:

0.00

AC:

AN:

42106

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

25622

East Asian (EAS)

AF:

0.00

AC:

AN:

39324

South Asian (SAS)

AF:

0.00

AC:

AN:

83876

European-Finnish (FIN)

AF:

0.00

AC:

AN:

53260

Middle Eastern (MID)

AF:

0.00

AC:

AN:

5650

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

1076116

Other (OTH)

AF:

0.00

AC:

AN:

58904

GnomAD4 genome

Cov.:

Alfa

AF:

0.00

Hom.:

Bravo

AF:

0.00000756

ClinVar

ClinVar submissions

Significance:Uncertain significance

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not specified (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.081

BayesDel_addAF

Benign

-0.20

BayesDel_noAF

Benign

-0.52

CADD

Benign

(source)

DANN

Benign

0.94

DEOGEN2

Benign

0.0031

Eigen

Benign

-0.010

Eigen_PC

Benign

0.10

FATHMM_MKL

Uncertain

0.92

LIST_S2

Benign

0.83

M_CAP

Benign

0.0074

MetaRNN

Benign

0.088

MetaSVM

Benign

-0.94

MutationAssessor

Benign

1.6

PhyloP100

1.8

PrimateAI

Benign

0.42

PROVEAN

Benign

-0.18

REVEL

Benign

0.071

Sift

Benign

0.31

Sift4G

Benign

0.38

Polyphen

0.51

Vest4

0.18

MutPred

0.46

Loss of sheet (P = 0.0104)

MVP

0.18

MPC

0.55

ClinPred

0.40

GERP RS

4.4

Varity_R

0.064

gMVP

0.33

Mutation Taster

=89/11

polymorphism

(source)

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over