12-76787261-A-G

Variant names:

• chr12-76787261-A-G
• rs4761444
• NM_015336.4:c.94-10173A>G

Variant summary

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

The NM_015336.4(ZDHHC17):​c.94-10173A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.458 in 151,940 control chromosomes in the GnomAD database, including 16,227 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 0.46 (16227 hom., cov: 31)
• Consequence: ZDHHC17 NM_015336.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.170
• Publications: 0 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.637 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZDHHC17	NM_015336.4	MANE Select	c.94-10173A>G		intron	N/A	NP_056151.2	Q8IUH5-1
	ZDHHC17	NM_001359626.1		c.64-10173A>G		intron	N/A	NP_001346555.1	A8KA01

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZDHHC17	ENST00000426126.7	TSL:1 MANE Select	c.94-10173A>G		intron	N/A	ENSP00000403397.2	Q8IUH5-1
	ZDHHC17	ENST00000968885.1		c.94-10173A>G		intron	N/A	ENSP00000638944.1
	ZDHHC17	ENST00000550876.1	TSL:4	c.54+5578A>G		intron	N/A	ENSP00000449734.1	F8VX48

Frequencies

GnomAD3 genomes AF: 0.457 AC: 69440 AN: 151822 Hom.: 16202 Cov.: 31

Gnomad AFR AF: 0.492

Gnomad AMI AF: 0.387

Gnomad AMR AF: 0.547

Gnomad ASJ AF: 0.471

Gnomad EAS AF: 0.655

Gnomad SAS AF: 0.412

Gnomad FIN AF: 0.430

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.408

Gnomad OTH AF: 0.452

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

GnomAD4 genome AF: 0.458 AC: 69515 AN: 151940 Hom.: 16227 Cov.: 31 AF XY: 0.462 AC XY: 34340 AN XY: 74268

African (AFR) AF: 0.493 AC: 20411 AN: 41430

American (AMR) AF: 0.547 AC: 8347 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.471 AC: 1634 AN: 3466

East Asian (EAS) AF: 0.655 AC: 3381 AN: 5160

South Asian (SAS) AF: 0.414 AC: 1991 AN: 4812

European-Finnish (FIN) AF: 0.430 AC: 4525 AN: 10528

Middle Eastern (MID) AF: 0.544 AC: 160 AN: 294

European-Non Finnish (NFE) AF: 0.409 AC: 27768 AN: 67974

Other (OTH) AF: 0.450 AC: 947 AN: 2106

Alfa AF: 0.426 Hom.: 10149

Bravo AF: 0.472

Asia WGS AF: 0.499 AC: 1731 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.44
DANN	Benign	0.57
PhyloP100		-0.17
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: rs4761444; hg19: chr12-77181041;