9-86323411-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.2339A>G(p.Asn780Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000328 in 1,614,092 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. 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.2339A>G | p.Asn780Ser | missense_variant | 13/27 | ENST00000375963.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TUT7 | ENST00000375963.8 | c.2339A>G | p.Asn780Ser | missense_variant | 13/27 | 5 | NM_024617.4 | P1 | |
TUT7 | ENST00000375960.6 | c.1970A>G | p.Asn657Ser | missense_variant | 9/20 | 1 | |||
TUT7 | ENST00000277141.10 | c.206A>G | p.Asn69Ser | missense_variant | 14/28 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.000177 AC: 27AN: 152234Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000131 AC: 33AN: 251352Hom.: 0 AF XY: 0.000110 AC XY: 15AN XY: 135834
GnomAD4 exome AF: 0.000343 AC: 502AN: 1461858Hom.: 0 Cov.: 33 AF XY: 0.000315 AC XY: 229AN XY: 727224
GnomAD4 genome ? AF: 0.000177 AC: 27AN: 152234Hom.: 0 Cov.: 32 AF XY: 0.000148 AC XY: 11AN XY: 74378
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 23, 2024 | The c.2339A>G (p.N780S) 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 2339, causing the asparagine (N) at amino acid position 780 to be replaced by a serine (S). 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