chr16-67394713-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.1346G>A(p.Arg449Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000463 in 1,339,746 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. R449R) has been classified 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.1346G>A | p.Arg449Gln | missense_variant | Exon 12 of 12 | 5 | NM_001323627.2 | ENSP00000459264.2 | ||
ZDHHC1 | ENST00000348579.6 | c.1411G>A | p.Asp471Asn | missense_variant | Exon 11 of 11 | 1 | ENSP00000340299.2 | |||
ZDHHC1 | ENST00000566075.1 | n.901G>A | non_coding_transcript_exon_variant | Exon 5 of 5 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000595 AC: 9AN: 151374Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.0000446 AC: 53AN: 1188372Hom.: 0 Cov.: 31 AF XY: 0.0000483 AC XY: 28AN XY: 579248
GnomAD4 genome AF: 0.0000595 AC: 9AN: 151374Hom.: 0 Cov.: 33 AF XY: 0.0000946 AC XY: 7AN XY: 73958
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1411G>A (p.D471N) alteration is located in exon 11 (coding exon 10) of the ZDHHC1 gene. This alteration results from a G to A substitution at nucleotide position 1411, causing the aspartic acid (D) at amino acid position 471 to be replaced by an asparagine (N). 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