rs2023627

chr8-17189217-C-T

Variant summary

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

The NM_016353.5(ZDHHC2):c.252+2792C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.81 in 148,202 control chromosomes in the GnomAD database, including 49,318 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 0.81 (49318 hom., cov: 22)
• Consequence: ZDHHC2 NM_016353.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.16

Genes affected

ZDHHC2 (HGNC:18469): (zinc finger DHHC-type palmitoyltransferase 2) Enables protein homodimerization activity and protein-cysteine S-palmitoyltransferase activity. Involved in several processes, including peptidyl-L-cysteine S-palmitoylation; regulation of protein catabolic process; and regulation of protein localization to plasma membrane. Located in Golgi apparatus and endoplasmic reticulum membrane. [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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.87 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZDHHC2	NM_016353.5	c.252+2792C>T		intron_variant		ENST00000262096.13

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZDHHC2	ENST00000262096.13	c.252+2792C>T		intron_variant		1	NM_016353.5	P1
ZDHHC2	ENST00000522184.1	c.117+2792C>T		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.810 AC: 120026 AN: 148108 Hom.: 49294 Cov.: 22

Gnomad AFR AF: 0.711

Gnomad AMI AF: 0.789

Gnomad AMR AF: 0.855

Gnomad ASJ AF: 0.863

Gnomad EAS AF: 0.589

Gnomad SAS AF: 0.720

Gnomad FIN AF: 0.839

Gnomad MID AF: 0.870

Gnomad NFE AF: 0.875

Gnomad OTH AF: 0.814

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

GnomAD4 genome AF: 0.810 AC: 120091 AN: 148202 Hom.: 49318 Cov.: 22 AF XY: 0.807 AC XY: 58102 AN XY: 71956

Gnomad4 AFR AF: 0.711

Gnomad4 AMR AF: 0.855

Gnomad4 ASJ AF: 0.863

Gnomad4 EAS AF: 0.589

Gnomad4 SAS AF: 0.720

Gnomad4 FIN AF: 0.839

Gnomad4 NFE AF: 0.875

Gnomad4 OTH AF: 0.810

Alfa AF: 0.857 Hom.: 73042

Bravo AF: 0.809

Asia WGS AF: 0.638 AC: 2221 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.27
Dann	Benign	0.38

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: rs2023627; hg19: chr8-17046726;