1-26850437-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_032283.3(ZDHHC18):āc.783G>Cā(p.Leu261Phe) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000991 in 1,613,776 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_032283.3 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZDHHC18 | NM_032283.3 | c.783G>C | p.Leu261Phe | missense_variant, splice_region_variant | 4/8 | ENST00000374142.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZDHHC18 | ENST00000374142.9 | c.783G>C | p.Leu261Phe | missense_variant, splice_region_variant | 4/8 | 1 | NM_032283.3 | P1 | |
ZDHHC18 | ENST00000374141.6 | c.378G>C | p.Leu126Phe | missense_variant, splice_region_variant | 4/8 | 2 | |||
ZDHHC18 | ENST00000488397.3 | c.78G>C | p.Leu26Phe | missense_variant, splice_region_variant | 1/7 | 2 | |||
ZDHHC18 | ENST00000534643.5 | c.378G>C | p.Leu126Phe | missense_variant, splice_region_variant | 4/6 | 4 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 151884Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 251470Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135904
GnomAD4 exome AF: 0.00000958 AC: 14AN: 1461892Hom.: 0 Cov.: 32 AF XY: 0.0000110 AC XY: 8AN XY: 727248
GnomAD4 genome AF: 0.0000132 AC: 2AN: 151884Hom.: 0 Cov.: 33 AF XY: 0.0000270 AC XY: 2AN XY: 74150
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 30, 2023 | The c.783G>C (p.L261F) alteration is located in exon 4 (coding exon 4) of the ZDHHC18 gene. This alteration results from a G to C substitution at nucleotide position 783, causing the leucine (L) at amino acid position 261 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