chr3-113954212-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001320466.2(ZDHHC23):c.674C>T(p.Pro225Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000149 in 1,614,046 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001320466.2 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZDHHC23 | NM_001320466.2 | c.674C>T | p.Pro225Leu | missense_variant | 3/5 | ENST00000638807.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZDHHC23 | ENST00000638807.2 | c.674C>T | p.Pro225Leu | missense_variant | 3/5 | 5 | NM_001320466.2 | P1 | |
ZDHHC23 | ENST00000330212.7 | c.674C>T | p.Pro225Leu | missense_variant | 3/6 | 1 | |||
ZDHHC23 | ENST00000498275.5 | c.656C>T | p.Pro219Leu | missense_variant | 4/7 | 2 | |||
ZDHHC23 | ENST00000478793.1 | c.674C>T | p.Pro225Leu | missense_variant, NMD_transcript_variant | 3/7 | 2 |
Frequencies
GnomAD3 genomes AF: 0.000105 AC: 16AN: 152170Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000637 AC: 16AN: 251286Hom.: 0 AF XY: 0.0000663 AC XY: 9AN XY: 135806
GnomAD4 exome AF: 0.000153 AC: 224AN: 1461876Hom.: 0 Cov.: 30 AF XY: 0.000144 AC XY: 105AN XY: 727238
GnomAD4 genome AF: 0.000105 AC: 16AN: 152170Hom.: 0 Cov.: 32 AF XY: 0.0000942 AC XY: 7AN XY: 74344
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 27, 2023 | The c.674C>T (p.P225L) alteration is located in exon 3 (coding exon 2) of the ZDHHC23 gene. This alteration results from a C to T substitution at nucleotide position 674, causing the proline (P) at amino acid position 225 to be replaced by a leucine (L). 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