rs9316337

Variant names:

• chr13-21388068-G-A
• rs9316337
• NM_001330059.2:c.728-434C>T

Variant summary

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

The NM_001330059.2(ZDHHC20):​c.728-434C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.513 in 151,830 control chromosomes in the GnomAD database, including 20,551 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 0.51 (20551 hom., cov: 31)
• Consequence: ZDHHC20 NM_001330059.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.97
• Publications: 4 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 = 0.586 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZDHHC20	NM_001330059.2	MANE Select	c.728-434C>T		intron	N/A	NP_001316988.1
	ZDHHC20	NM_153251.4		c.728-434C>T		intron	N/A	NP_694983.2
	ZDHHC20	NM_001286638.2		c.539-434C>T		intron	N/A	NP_001273567.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZDHHC20	ENST00000400590.8	TSL:5 MANE Select	c.728-434C>T		intron	N/A	ENSP00000383433.3
	ZDHHC20	ENST00000382466.7	TSL:1	c.728-434C>T		intron	N/A	ENSP00000371905.3
	ZDHHC20	ENST00000320220.13	TSL:1	c.728-434C>T		intron	N/A	ENSP00000313583.9

Frequencies

GnomAD3 genomes AF: 0.513 AC: 77806 AN: 151710 Hom.: 20528 Cov.: 31

Gnomad AFR AF: 0.434

Gnomad AMI AF: 0.679

Gnomad AMR AF: 0.485

Gnomad ASJ AF: 0.506

Gnomad EAS AF: 0.263

Gnomad SAS AF: 0.428

Gnomad FIN AF: 0.514

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.590

Gnomad OTH AF: 0.503

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

GnomAD4 genome AF: 0.513 AC: 77874 AN: 151830 Hom.: 20551 Cov.: 31 AF XY: 0.506 AC XY: 37572 AN XY: 74192

African (AFR) AF: 0.434 AC: 17969 AN: 41378

American (AMR) AF: 0.485 AC: 7385 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.506 AC: 1754 AN: 3468

East Asian (EAS) AF: 0.263 AC: 1358 AN: 5162

South Asian (SAS) AF: 0.429 AC: 2069 AN: 4820

European-Finnish (FIN) AF: 0.514 AC: 5393 AN: 10494

Middle Eastern (MID) AF: 0.517 AC: 152 AN: 294

European-Non Finnish (NFE) AF: 0.591 AC: 40126 AN: 67952

Other (OTH) AF: 0.497 AC: 1049 AN: 2112

Alfa AF: 0.544 Hom.: 3170

Bravo AF: 0.512

Asia WGS AF: 0.344 AC: 1198 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	0.063
DANN	Benign	0.49
PhyloP100		-2.0
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: rs9316337; hg19: chr13-21962207;