rs9316335

Variant names:

• chr13-21384779-A-C
• rs9316335
• NM_001330059.2:c.855-1770T>G

Variant summary

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

The NM_001330059.2(ZDHHC20):​c.855-1770T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.582 in 151,940 control chromosomes in the GnomAD database, including 26,881 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 0.58 (26881 hom., cov: 31)
• Consequence: ZDHHC20 NM_001330059.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0220
• Publications: 2 publications found

Genes affected

ZDHHC20 (HGNC:20749): (zinc finger DHHC-type palmitoyltransferase 20) Enables protein-cysteine S-palmitoyltransferase activity and zinc ion binding activity. Involved in peptidyl-L-cysteine S-palmitoylation. Located in intracellular membrane-bounded organelle and plasma membrane. Is integral component of Golgi membrane. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000291046 (HGNC:):

MIPEPP3 (HGNC:39458): (mitochondrial intermediate peptidase pseudogene 3)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.682 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001330059.2. 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
	ZDHHC20	NM_001330059.2	MANE Select	c.855-1770T>G		intron	N/A	NP_001316988.1	Q5W0Z9-1
	ZDHHC20	NM_153251.4		c.855-1770T>G		intron	N/A	NP_694983.2
	ZDHHC20	NM_001286638.2		c.666-1770T>G		intron	N/A	NP_001273567.1	B4DRN8

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZDHHC20	ENST00000400590.8	TSL:5 MANE Select	c.855-1770T>G		intron	N/A	ENSP00000383433.3	Q5W0Z9-1
	ZDHHC20	ENST00000382466.7	TSL:1	c.855-1770T>G		intron	N/A	ENSP00000371905.3	Q5W0Z9-3
	ZDHHC20	ENST00000320220.13	TSL:1	c.855-1770T>G		intron	N/A	ENSP00000313583.9	Q5W0Z9-4

Frequencies

GnomAD3 genomes AF: 0.582 AC: 88305 AN: 151822 Hom.: 26863 Cov.: 31

Gnomad AFR AF: 0.451

Gnomad AMI AF: 0.753

Gnomad AMR AF: 0.526

Gnomad ASJ AF: 0.602

Gnomad EAS AF: 0.265

Gnomad SAS AF: 0.484

Gnomad FIN AF: 0.677

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.687

Gnomad OTH AF: 0.560

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

GnomAD4 genome AF: 0.582 AC: 88367 AN: 151940 Hom.: 26881 Cov.: 31 AF XY: 0.576 AC XY: 42803 AN XY: 74250

African (AFR) AF: 0.451 AC: 18678 AN: 41406

American (AMR) AF: 0.525 AC: 8018 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.602 AC: 2088 AN: 3468

East Asian (EAS) AF: 0.266 AC: 1368 AN: 5152

South Asian (SAS) AF: 0.485 AC: 2332 AN: 4810

European-Finnish (FIN) AF: 0.677 AC: 7148 AN: 10556

Middle Eastern (MID) AF: 0.568 AC: 167 AN: 294

European-Non Finnish (NFE) AF: 0.687 AC: 46717 AN: 67964

Other (OTH) AF: 0.553 AC: 1164 AN: 2106

Alfa AF: 0.647 Hom.: 27960

Bravo AF: 0.568

Asia WGS AF: 0.366 AC: 1275 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.7
DANN	Benign	0.56
PhyloP100		-0.022
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: rs9316335; hg19: chr13-21958918;