9-86322889-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_024617.4(TUT7):āc.2861T>Cā(p.Ile954Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000005 in 1,600,280 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.
Frequency
Consequence
NM_024617.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TUT7 | ENST00000375963.8 | c.2861T>C | p.Ile954Thr | missense_variant | Exon 13 of 27 | 5 | NM_024617.4 | ENSP00000365130.3 | ||
TUT7 | ENST00000375960.6 | c.2492T>C | p.Ile831Thr | missense_variant | Exon 9 of 20 | 1 | ENSP00000365127.2 | |||
TUT7 | ENST00000277141.10 | c.728T>C | p.Ile243Thr | missense_variant | Exon 14 of 28 | 2 | ENSP00000277141.6 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152194Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000418 AC: 1AN: 239044Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 128964
GnomAD4 exome AF: 0.00000483 AC: 7AN: 1448086Hom.: 0 Cov.: 31 AF XY: 0.00000695 AC XY: 5AN XY: 719558
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152194Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74340
ClinVar
Submissions by phenotype
not specified Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at