rs2023627

Variant names:

• chr8-17189217-C-T
• rs2023627
• NM_016353.5:c.252+2792C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
ZDHHC2	NM_016353.5	c.252+2792C>T		intron_variant	Intron 3 of 12	ENST00000262096.13	NP_057437.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZDHHC2	ENST00000262096.13	c.252+2792C>T		intron_variant	Intron 3 of 12	1	NM_016353.5	ENSP00000262096.8
ZDHHC2	ENST00000522184.1	c.117+2792C>T		intron_variant	Intron 3 of 6	3		ENSP00000430317.1

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

African (AFR) AF: 0.711 AC: 28445 AN: 40016

American (AMR) AF: 0.855 AC: 12660 AN: 14810

Ashkenazi Jewish (ASJ) AF: 0.863 AC: 2993 AN: 3470

East Asian (EAS) AF: 0.589 AC: 2938 AN: 4988

South Asian (SAS) AF: 0.720 AC: 3346 AN: 4650

European-Finnish (FIN) AF: 0.839 AC: 8033 AN: 9570

Middle Eastern (MID) AF: 0.860 AC: 246 AN: 286

European-Non Finnish (NFE) AF: 0.875 AC: 59057 AN: 67460

Other (OTH) AF: 0.810 AC: 1663 AN: 2052

Alfa AF: 0.847 Hom.: 98488

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
PhyloP100		-1.2
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2023627; hg19: chr8-17046726;