9-86303134-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 3P and 1B. PM2PP2BP4
The NM_024617.4(TUT7):c.4046T>C(p.Ile1349Thr) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 32)
Consequence
TUT7
NM_024617.4 missense
NM_024617.4 missense
Scores
2
9
6
Clinical Significance
Conservation
PhyloP100: 5.77
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]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
PP2
?
Missense variant where missense usually causes diseases, TUT7
BP4
?
Computational evidence support a benign effect (MetaRNN=0.3020355).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TUT7 | NM_024617.4 | c.4046T>C | p.Ile1349Thr | missense_variant | 25/27 | ENST00000375963.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TUT7 | ENST00000375963.8 | c.4046T>C | p.Ile1349Thr | missense_variant | 25/27 | 5 | NM_024617.4 | P1 | |
TUT7 | ENST00000375960.6 | c.3338T>C | p.Ile1113Thr | missense_variant | 18/20 | 1 | |||
TUT7 | ENST00000277141.10 | c.1913T>C | p.Ile638Thr | missense_variant | 26/28 | 2 | |||
TUT7 | ENST00000375957.5 | c.746T>C | p.Ile249Thr | missense_variant | 10/12 | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
Cov.:
32
GnomAD4 exome Cov.: 29
GnomAD4 exome
Cov.:
29
GnomAD4 genome ? Cov.: 32
GnomAD4 genome
?
Cov.:
32
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 21, 2023 | The c.4046T>C (p.I1349T) alteration is located in exon 25 (coding exon 24) of the ZCCHC6 gene. This alteration results from a T to C substitution at nucleotide position 4046, causing the isoleucine (I) at amino acid position 1349 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Uncertain
D
BayesDel_noAF
Benign
Cadd
Uncertain
Dann
Uncertain
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T;T;T;T
M_CAP
Benign
D
MetaRNN
Benign
T;T;T;T
MetaSVM
Uncertain
T
MutationTaster
Benign
D;D;D;D;D
PrimateAI
Pathogenic
D
PROVEAN
Uncertain
D;D;D;D
REVEL
Uncertain
Sift
Benign
D;T;T;D
Sift4G
Uncertain
D;T;T;T
Polyphen
0.85, 0.89
.;P;.;P
Vest4
MutPred
0.47
.;.;.;Gain of disorder (P = 0.0342);
MVP
MPC
0.95
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.