rs6795707

chr3-196210539-G-T

Variant summary

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

The NM_001039617.2(ZDHHC19):c.268+77C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.151 in 1,596,488 control chromosomes in the GnomAD database, including 20,077 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 0.13 (1646 hom., cov: 32)
  • Exomes 𝑓: 0.15 (18431 hom.)
• Consequence: ZDHHC19 NM_001039617.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.537

Genes affected

ZDHHC19 (HGNC:20713): (zinc finger DHHC-type palmitoyltransferase 19) Enables protein-cysteine S-palmitoyltransferase activity. Involved in peptidyl-L-cysteine S-palmitoylation. Located in Golgi membrane; endoplasmic reticulum; and perinucleolar compartment. [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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.338 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZDHHC19	NM_001039617.2	c.268+77C>A		intron_variant		ENST00000296326.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZDHHC19	ENST00000296326.8	c.268+77C>A		intron_variant		5	NM_001039617.2	P1

Frequencies

GnomAD3 genomes AF: 0.125 AC: 19050 AN: 152116 Hom.: 1648 Cov.: 32

Gnomad AFR AF: 0.0353

Gnomad AMI AF: 0.116

Gnomad AMR AF: 0.196

Gnomad ASJ AF: 0.141

Gnomad EAS AF: 0.351

Gnomad SAS AF: 0.201

Gnomad FIN AF: 0.146

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.137

Gnomad OTH AF: 0.127

GnomAD4 exome AF: 0.153 AC: 221293 AN: 1444254 Hom.: 18431 AF XY: 0.154 AC XY: 110185 AN XY: 717706

Gnomad4 AFR exome AF: 0.0291

Gnomad4 AMR exome AF: 0.238

Gnomad4 ASJ exome AF: 0.144

Gnomad4 EAS exome AF: 0.343

Gnomad4 SAS exome AF: 0.187

Gnomad4 FIN exome AF: 0.140

Gnomad4 NFE exome AF: 0.145

Gnomad4 OTH exome AF: 0.156

GnomAD4 genome AF: 0.125 AC: 19039 AN: 152234 Hom.: 1646 Cov.: 32 AF XY: 0.129 AC XY: 9602 AN XY: 74434

Gnomad4 AFR AF: 0.0352

Gnomad4 AMR AF: 0.196

Gnomad4 ASJ AF: 0.141

Gnomad4 EAS AF: 0.351

Gnomad4 SAS AF: 0.201

Gnomad4 FIN AF: 0.146

Gnomad4 NFE AF: 0.137

Gnomad4 OTH AF: 0.125

Alfa AF: 0.136 Hom.: 740

Bravo AF: 0.128

Asia WGS AF: 0.217 AC: 754 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	5.8
Dann	Benign	0.53

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: rs6795707; hg19: chr3-195937410;