chr12-76827906-T-C

Variant names:

• chr12-76827906-T-C
• rs10778948
• NM_015336.4:c.1041-484T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_015336.4(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 NM_015336.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.302
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015336.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZDHHC17	NM_015336.4	MANE Select	c.1041-484T>C		intron	N/A	NP_056151.2
	ZDHHC17	NM_001359626.1		c.1011-484T>C		intron	N/A	NP_001346555.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZDHHC17	ENST00000426126.7	TSL:1 MANE Select	c.1041-484T>C		intron	N/A	ENSP00000403397.2

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

African (AFR) AF: 0.592 AC: 24525 AN: 41432

American (AMR) AF: 0.655 AC: 10005 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.609 AC: 2112 AN: 3468

East Asian (EAS) AF: 0.675 AC: 3488 AN: 5168

South Asian (SAS) AF: 0.511 AC: 2465 AN: 4824

European-Finnish (FIN) AF: 0.661 AC: 6964 AN: 10538

Middle Eastern (MID) AF: 0.634 AC: 185 AN: 292

European-Non Finnish (NFE) AF: 0.609 AC: 41346 AN: 67842

Other (OTH) AF: 0.594 AC: 1254 AN: 2112

Alfa AF: 0.606 Hom.: 14268

Bravo AF: 0.615

Asia WGS AF: 0.583 AC: 2020 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	7.1
DANN	Benign	0.84
PhyloP100		-0.30
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: rs10778948; hg19: chr12-77221686;