chrX-112455083-A-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_001395362.2(RTL4):c.355A>T(p.Ser119Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000107 in 1,210,084 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 4 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 12/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001395362.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RTL4 | NM_001395362.2 | c.355A>T | p.Ser119Cys | missense_variant | 5/5 | ENST00000695839.1 | |
RTL4 | NM_001004308.3 | c.355A>T | p.Ser119Cys | missense_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RTL4 | ENST00000695839.1 | c.355A>T | p.Ser119Cys | missense_variant | 5/5 | NM_001395362.2 | P1 | ||
RTL4 | ENST00000340433.4 | c.355A>T | p.Ser119Cys | missense_variant | 4/4 | P1 | |||
RTL4 | ENST00000695808.1 | c.355A>T | p.Ser119Cys | missense_variant | 3/3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000893 AC: 1AN: 111998Hom.: 0 Cov.: 22 AF XY: 0.0000293 AC XY: 1AN XY: 34152
GnomAD4 exome AF: 0.0000109 AC: 12AN: 1098086Hom.: 0 Cov.: 34 AF XY: 0.00000825 AC XY: 3AN XY: 363468
GnomAD4 genome ? AF: 0.00000893 AC: 1AN: 111998Hom.: 0 Cov.: 22 AF XY: 0.0000293 AC XY: 1AN XY: 34152
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 14, 2023 | The c.355A>T (p.S119C) 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 355, causing the serine (S) at amino acid position 119 to be replaced by a cysteine (C). 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