6-157664252-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_024630.3(ZDHHC14):c.1069-8472T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.181 in 152,244 control chromosomes in the GnomAD database, including 2,972 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.18 (2972 hom., cov: 33)
• Consequence: ZDHHC14 NM_024630.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.31

Genes affected

ZDHHC14 (HGNC:20341): (zinc finger DHHC-type palmitoyltransferase 14) Enables palmitoyltransferase activity. Involved in peptidyl-L-cysteine S-palmitoylation. Located in endoplasmic reticulum. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.504 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZDHHC14	NM_024630.3	c.1069-8472T>C		intron_variant		ENST00000359775.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZDHHC14	ENST00000359775.10	c.1069-8472T>C		intron_variant		1	NM_024630.3	A1

Frequencies

GnomAD3 genomes AF: 0.181 AC: 27549 AN: 152126 Hom.: 2974 Cov.: 33

Gnomad AFR AF: 0.145

Gnomad AMI AF: 0.134

Gnomad AMR AF: 0.154

Gnomad ASJ AF: 0.209

Gnomad EAS AF: 0.520

Gnomad SAS AF: 0.272

Gnomad FIN AF: 0.141

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.181

Gnomad OTH AF: 0.193

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.181 AC: 27548 AN: 152244 Hom.: 2972 Cov.: 33 AF XY: 0.182 AC XY: 13531 AN XY: 74448

Gnomad4 AFR AF: 0.145

Gnomad4 AMR AF: 0.154

Gnomad4 ASJ AF: 0.209

Gnomad4 EAS AF: 0.520

Gnomad4 SAS AF: 0.273

Gnomad4 FIN AF: 0.141

Gnomad4 NFE AF: 0.181

Gnomad4 OTH AF: 0.195

Alfa AF: 0.184 Hom.: 3892

Bravo AF: 0.184

Asia WGS AF: 0.371 AC: 1292 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.70
Dann	Benign	0.50

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs9365242; hg19: chr6-158085284; COSMIC: COSV58196514;