chrX-112454900-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001395362.2(RTL4):c.172C>T(p.Leu58Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000447 in 1,208,699 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 13 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
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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.172C>T | p.Leu58Phe | missense_variant | 5/5 | ENST00000695839.1 | |
RTL4 | NM_001004308.3 | c.172C>T | p.Leu58Phe | missense_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RTL4 | ENST00000695839.1 | c.172C>T | p.Leu58Phe | missense_variant | 5/5 | NM_001395362.2 | P1 | ||
RTL4 | ENST00000340433.4 | c.172C>T | p.Leu58Phe | missense_variant | 4/4 | P1 | |||
RTL4 | ENST00000695808.1 | c.172C>T | p.Leu58Phe | missense_variant | 3/3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000233 AC: 26AN: 111522Hom.: 0 Cov.: 23 AF XY: 0.000178 AC XY: 6AN XY: 33690
GnomAD3 exomes AF: 0.0000165 AC: 3AN: 181668Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 66420
GnomAD4 exome AF: 0.0000255 AC: 28AN: 1097124Hom.: 0 Cov.: 34 AF XY: 0.0000193 AC XY: 7AN XY: 362558
GnomAD4 genome ? AF: 0.000233 AC: 26AN: 111575Hom.: 0 Cov.: 23 AF XY: 0.000178 AC XY: 6AN XY: 33753
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 30, 2021 | The c.172C>T (p.L58F) alteration is located in exon 3 (coding exon 1) of the ZCCHC16 gene. This alteration results from a C to T substitution at nucleotide position 172, causing the leucine (L) at amino acid position 58 to be replaced by a phenylalanine (F). 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