chr12-76827906-T-C

Position:

• chr12-76827906-T-C

Variant summary

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

The ENST00000426126.7(ZDHHC17):​c.1041-484T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.611 in 151,858 control chromosomes in the GnomAD database, including 28,418 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 0.61 (28418 hom., cov: 31)
• Consequence: ZDHHC17 ENST00000426126.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.302

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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.656 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZDHHC17	NM_015336.4	c.1041-484T>C		intron_variant		ENST00000426126.7	NP_056151.2
ZDHHC17	NM_001359626.1	c.1011-484T>C		intron_variant			NP_001346555.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZDHHC17	ENST00000426126.7	c.1041-484T>C		intron_variant		1	NM_015336.4	ENSP00000403397	P1

Frequencies

GnomAD3 genomes AF: 0.611 AC: 92727 AN: 151740 Hom.: 28395 Cov.: 31

Gnomad AFR AF: 0.592

Gnomad AMI AF: 0.513

Gnomad AMR AF: 0.655

Gnomad ASJ AF: 0.609

Gnomad EAS AF: 0.675

Gnomad SAS AF: 0.509

Gnomad FIN AF: 0.661

Gnomad MID AF: 0.640

Gnomad NFE AF: 0.609

Gnomad OTH AF: 0.597

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

GnomAD4 genome AF: 0.611 AC: 92809 AN: 151858 Hom.: 28418 Cov.: 31 AF XY: 0.614 AC XY: 45587 AN XY: 74210

Gnomad4 AFR AF: 0.592

Gnomad4 AMR AF: 0.655

Gnomad4 ASJ AF: 0.609

Gnomad4 EAS AF: 0.675

Gnomad4 SAS AF: 0.511

Gnomad4 FIN AF: 0.661

Gnomad4 NFE AF: 0.609

Gnomad4 OTH AF: 0.594

Alfa AF: 0.606 Hom.: 12721

Bravo AF: 0.615

Asia WGS AF: 0.583 AC: 2020 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	7.1
DANN	Benign	0.84

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: rs10778948; hg19: chr12-77221686;