chr16-67398276-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001323627.2(ZDHHC1):c.863C>A(p.Pro288Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000372 in 1,614,012 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 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 Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ZDHHC1 | NM_001323627.2 | c.863C>A | p.Pro288Gln | missense_variant | 8/12 | ENST00000565726.3 | NP_001310556.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ZDHHC1 | ENST00000565726.3 | c.863C>A | p.Pro288Gln | missense_variant | 8/12 | 5 | NM_001323627.2 | ENSP00000459264 | P1 | |
ZDHHC1 | ENST00000348579.6 | c.863C>A | p.Pro288Gln | missense_variant | 8/11 | 1 | ENSP00000340299 | |||
ZDHHC1 | ENST00000562122.1 | n.481C>A | non_coding_transcript_exon_variant | 5/6 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152214Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251244Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135770
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1461798Hom.: 0 Cov.: 34 AF XY: 0.00000413 AC XY: 3AN XY: 727194
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152214Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74364
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 07, 2023 | The c.863C>A (p.P288Q) alteration is located in exon 8 (coding exon 7) of the ZDHHC1 gene. This alteration results from a C to A substitution at nucleotide position 863, causing the proline (P) at amino acid position 288 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