chrX-112455601-A-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001395362.2(RTL4):c.873A>T(p.Arg291Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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. R291K) has been classified as Likely benign.
Frequency
Consequence
NM_001395362.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RTL4 | NM_001395362.2 | c.873A>T | p.Arg291Ser | missense_variant | 5/5 | ENST00000695839.1 | |
RTL4 | NM_001004308.3 | c.873A>T | p.Arg291Ser | missense_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RTL4 | ENST00000695839.1 | c.873A>T | p.Arg291Ser | missense_variant | 5/5 | NM_001395362.2 | P1 | ||
RTL4 | ENST00000340433.4 | c.873A>T | p.Arg291Ser | missense_variant | 4/4 | P1 | |||
RTL4 | ENST00000695808.1 | c.873A>T | p.Arg291Ser | missense_variant | 3/3 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 23
GnomAD4 exome Cov.: 32
GnomAD4 genome ? Cov.: 23
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 01, 2022 | The c.873A>T (p.R291S) alteration is located in exon 3 (coding exon 1) of the ZCCHC16 gene. This alteration results from a A to T substitution at nucleotide position 873, causing the arginine (R) at amino acid position 291 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
Publications
No publications associated with this variant yet.