chr6-157653560-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_024630.3(ZDHHC14):c.1001C>T(p.Thr334Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00312 in 1,613,990 control chromosomes in the GnomAD database, including 18 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in the same amino acid substitution has been previously reported as Likely benign in UniProt.
Frequency
Consequence
NM_024630.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00223 AC: 339AN: 152194Hom.: 4 Cov.: 32
GnomAD3 exomes AF: 0.00281 AC: 706AN: 251092Hom.: 4 AF XY: 0.00263 AC XY: 357AN XY: 135730
GnomAD4 exome AF: 0.00321 AC: 4692AN: 1461678Hom.: 14 Cov.: 31 AF XY: 0.00305 AC XY: 2216AN XY: 727150
GnomAD4 genome AF: 0.00222 AC: 338AN: 152312Hom.: 4 Cov.: 32 AF XY: 0.00219 AC XY: 163AN XY: 74484
ClinVar
Submissions by phenotype
not provided Benign:1
ZDHHC14: BP4, BS1, BS2 -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at