9-86323157-T-C
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 3P and 4B. PM2PP2BP4_Strong
The NM_024617.4(TUT7):c.2593A>G(p.Asn865Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000052 in 1,614,176 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_024617.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TUT7 | NM_024617.4 | c.2593A>G | p.Asn865Asp | missense_variant | 13/27 | ENST00000375963.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TUT7 | ENST00000375963.8 | c.2593A>G | p.Asn865Asp | missense_variant | 13/27 | 5 | NM_024617.4 | P1 | |
TUT7 | ENST00000375960.6 | c.2224A>G | p.Asn742Asp | missense_variant | 9/20 | 1 | |||
TUT7 | ENST00000277141.10 | c.460A>G | p.Asn154Asp | missense_variant | 14/28 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000460 AC: 7AN: 152188Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000104 AC: 26AN: 251052Hom.: 1 AF XY: 0.0000885 AC XY: 12AN XY: 135660
GnomAD4 exome AF: 0.0000527 AC: 77AN: 1461870Hom.: 1 Cov.: 33 AF XY: 0.0000564 AC XY: 41AN XY: 727234
GnomAD4 genome ? AF: 0.0000460 AC: 7AN: 152306Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74482
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 12, 2023 | The c.2593A>G (p.N865D) alteration is located in exon 13 (coding exon 12) of the ZCCHC6 gene. This alteration results from a A to G substitution at nucleotide position 2593, causing the asparagine (N) at amino acid position 865 to be replaced by an aspartic acid (D). 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