chr9-86319641-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 3P and 2B. PM2PP2BP4_Moderate
The NM_024617.4(TUT7):āc.3058C>Gā(p.Gln1020Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000311 in 1,608,702 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_024617.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TUT7 | NM_024617.4 | c.3058C>G | p.Gln1020Glu | missense_variant | 15/27 | ENST00000375963.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TUT7 | ENST00000375963.8 | c.3058C>G | p.Gln1020Glu | missense_variant | 15/27 | 5 | NM_024617.4 | P1 | |
TUT7 | ENST00000375960.6 | c.2509-2365C>G | intron_variant | 1 | |||||
TUT7 | ENST00000277141.10 | c.925C>G | p.Gln309Glu | missense_variant | 16/28 | 2 | |||
TUT7 | ENST00000375957.5 | c.-129C>G | 5_prime_UTR_variant | 1/12 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152136Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000121 AC: 3AN: 246946Hom.: 0 AF XY: 0.0000150 AC XY: 2AN XY: 133498
GnomAD4 exome AF: 0.00000206 AC: 3AN: 1456566Hom.: 0 Cov.: 29 AF XY: 0.00000414 AC XY: 3AN XY: 724262
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152136Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74320
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 17, 2023 | The c.3058C>G (p.Q1020E) alteration is located in exon 15 (coding exon 14) of the ZCCHC6 gene. This alteration results from a C to G substitution at nucleotide position 3058, causing the glutamine (Q) at amino acid position 1020 to be replaced by a glutamic acid (E). 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