9-86301591-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 3P and 1B. PM2PP2BP4
The NM_024617.4(TUT7):c.4105C>T(p.Arg1369Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000479 in 1,460,904 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R1369Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_024617.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TUT7 | NM_024617.4 | c.4105C>T | p.Arg1369Trp | missense_variant | 26/27 | ENST00000375963.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TUT7 | ENST00000375963.8 | c.4105C>T | p.Arg1369Trp | missense_variant | 26/27 | 5 | NM_024617.4 | P1 | |
TUT7 | ENST00000375960.6 | c.3397C>T | p.Arg1133Trp | missense_variant | 19/20 | 1 | |||
TUT7 | ENST00000277141.10 | c.1972C>T | p.Arg658Trp | missense_variant | 27/28 | 2 | |||
TUT7 | ENST00000375957.5 | c.805C>T | p.Arg269Trp | missense_variant | 11/12 | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.00000799 AC: 2AN: 250382Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135404
GnomAD4 exome AF: 0.00000479 AC: 7AN: 1460904Hom.: 0 Cov.: 31 AF XY: 0.00000550 AC XY: 4AN XY: 726836
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 26, 2022 | The c.4105C>T (p.R1369W) alteration is located in exon 26 (coding exon 25) of the ZCCHC6 gene. This alteration results from a C to T substitution at nucleotide position 4105, causing the arginine (R) at amino acid position 1369 to be replaced by a tryptophan (W). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at