16-67398222-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001323627.2(ZDHHC1):c.917G>A(p.Arg306Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000297 in 1,614,138 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001323627.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ZDHHC1 | ENST00000565726.3 | c.917G>A | p.Arg306Gln | missense_variant | Exon 8 of 12 | 5 | NM_001323627.2 | ENSP00000459264.2 | ||
ZDHHC1 | ENST00000348579.6 | c.917G>A | p.Arg306Gln | missense_variant | Exon 8 of 11 | 1 | ENSP00000340299.2 | |||
ZDHHC1 | ENST00000562122.1 | n.535G>A | non_coding_transcript_exon_variant | Exon 5 of 6 | 2 |
Frequencies
GnomAD3 genomes AF: 0.000131 AC: 20AN: 152212Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000438 AC: 11AN: 251264Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135802
GnomAD4 exome AF: 0.0000198 AC: 29AN: 1461808Hom.: 0 Cov.: 34 AF XY: 0.0000165 AC XY: 12AN XY: 727212
GnomAD4 genome AF: 0.000125 AC: 19AN: 152330Hom.: 0 Cov.: 33 AF XY: 0.000161 AC XY: 12AN XY: 74498
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.917G>A (p.R306Q) alteration is located in exon 8 (coding exon 7) of the ZDHHC1 gene. This alteration results from a G to A substitution at nucleotide position 917, causing the arginine (R) at amino acid position 306 to be replaced by a glutamine (Q). 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