rs11115332

Positions:

• chr12-76777412-C-G
• chr12-76777412-C-T

Variant summary

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

The NM_015336.4(ZDHHC17):​c.93+13083C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.079 in 152,100 control chromosomes in the GnomAD database, including 629 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 0.079 (629 hom., cov: 32)
• Consequence: ZDHHC17 NM_015336.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.42

Genes affected

ZDHHC17 (HGNC:18412): (zinc finger DHHC-type palmitoyltransferase 17) Enables identical protein binding activity and protein-cysteine S-palmitoyltransferase activity. Involved in lipoprotein transport and protein palmitoylation. Located in Golgi membrane; Golgi-associated vesicle membrane; and aggresome. [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=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.147 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZDHHC17	NM_015336.4	c.93+13083C>G		intron_variant		ENST00000426126.7
ZDHHC17	NM_001359626.1	c.63+13083C>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZDHHC17	ENST00000426126.7	c.93+13083C>G		intron_variant		1	NM_015336.4	P1

Frequencies

GnomAD3 genomes AF: 0.0790 AC: 12009 AN: 151980 Hom.: 629 Cov.: 32

Gnomad AFR AF: 0.140

Gnomad AMI AF: 0.0417

Gnomad AMR AF: 0.0522

Gnomad ASJ AF: 0.0461

Gnomad EAS AF: 0.156

Gnomad SAS AF: 0.123

Gnomad FIN AF: 0.0470

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0462

Gnomad OTH AF: 0.0768

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

GnomAD4 genome AF: 0.0790 AC: 12014 AN: 152100 Hom.: 629 Cov.: 32 AF XY: 0.0794 AC XY: 5901 AN XY: 74362

Gnomad4 AFR AF: 0.140

Gnomad4 AMR AF: 0.0521

Gnomad4 ASJ AF: 0.0461

Gnomad4 EAS AF: 0.156

Gnomad4 SAS AF: 0.123

Gnomad4 FIN AF: 0.0470

Gnomad4 NFE AF: 0.0462

Gnomad4 OTH AF: 0.0764

Alfa AF: 0.0262 Hom.: 20

Bravo AF: 0.0818

Asia WGS AF: 0.134 AC: 464 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.40
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: rs11115332; hg19: chr12-77171192;