chrX-112454907-A-G
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001395362.2(RTL4):c.179A>G(p.His60Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000571 in 1,208,463 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 23 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 13/19 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
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RTL4 | NM_001395362.2 | c.179A>G | p.His60Arg | missense_variant | 5/5 | ENST00000695839.1 | |
RTL4 | NM_001004308.3 | c.179A>G | p.His60Arg | missense_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RTL4 | ENST00000695839.1 | c.179A>G | p.His60Arg | missense_variant | 5/5 | NM_001395362.2 | P1 | ||
RTL4 | ENST00000340433.4 | c.179A>G | p.His60Arg | missense_variant | 4/4 | P1 | |||
RTL4 | ENST00000695808.1 | c.179A>G | p.His60Arg | missense_variant | 3/3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000395 AC: 44AN: 111297Hom.: 0 Cov.: 22 AF XY: 0.000418 AC XY: 14AN XY: 33497
GnomAD3 exomes AF: 0.000105 AC: 19AN: 181535Hom.: 0 AF XY: 0.000136 AC XY: 9AN XY: 66299
GnomAD4 exome AF: 0.0000228 AC: 25AN: 1097110Hom.: 0 Cov.: 34 AF XY: 0.0000248 AC XY: 9AN XY: 362546
GnomAD4 genome ? AF: 0.000395 AC: 44AN: 111353Hom.: 0 Cov.: 22 AF XY: 0.000417 AC XY: 14AN XY: 33563
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 14, 2022 | The c.179A>G (p.H60R) alteration is located in exon 3 (coding exon 1) of the ZCCHC16 gene. This alteration results from a A to G substitution at nucleotide position 179, causing the histidine (H) at amino acid position 60 to be replaced by an arginine (R). 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