X-112455021-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_001395362.2(RTL4):c.293T>C(p.Leu98Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000894 in 111,795 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001395362.2 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RTL4 | NM_001395362.2 | c.293T>C | p.Leu98Pro | missense_variant | 5/5 | ENST00000695839.1 | |
RTL4 | NM_001004308.3 | c.293T>C | p.Leu98Pro | missense_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RTL4 | ENST00000695839.1 | c.293T>C | p.Leu98Pro | missense_variant | 5/5 | NM_001395362.2 | P1 | ||
RTL4 | ENST00000340433.4 | c.293T>C | p.Leu98Pro | missense_variant | 4/4 | P1 | |||
RTL4 | ENST00000695808.1 | c.293T>C | p.Leu98Pro | missense_variant | 3/3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000894 AC: 1AN: 111795Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 33963
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1098165Hom.: 0 Cov.: 34 AF XY: 0.00 AC XY: 0AN XY: 363553
GnomAD4 genome ? AF: 0.00000894 AC: 1AN: 111795Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 33963
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 07, 2024 | The c.293T>C (p.L98P) alteration is located in exon 3 (coding exon 1) of the ZCCHC16 gene. This alteration results from a T to C substitution at nucleotide position 293, causing the leucine (L) at amino acid position 98 to be replaced by a proline (P). 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