rs1409071

Variant names:

• chr13-21388634-A-G
• rs1409071
• NM_001330059.2:c.728-1000T>C

Variant summary

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

The NM_001330059.2(ZDHHC20):​c.728-1000T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.509 in 152,052 control chromosomes in the GnomAD database, including 20,253 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 (20253 hom., cov: 32)
• Consequence: ZDHHC20 NM_001330059.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.41
• Publications: 5 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 = 0.579 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZDHHC20	NM_001330059.2	c.728-1000T>C		intron_variant	Intron 8 of 12	ENST00000400590.8	NP_001316988.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZDHHC20	ENST00000400590.8	c.728-1000T>C		intron_variant	Intron 8 of 12	5	NM_001330059.2	ENSP00000383433.3

Frequencies

GnomAD3 genomes AF: 0.509 AC: 77316 AN: 151934 Hom.: 20231 Cov.: 32

Gnomad AFR AF: 0.432

Gnomad AMI AF: 0.678

Gnomad AMR AF: 0.483

Gnomad ASJ AF: 0.507

Gnomad EAS AF: 0.262

Gnomad SAS AF: 0.426

Gnomad FIN AF: 0.511

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.584

Gnomad OTH AF: 0.500

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

GnomAD4 genome AF: 0.509 AC: 77381 AN: 152052 Hom.: 20253 Cov.: 32 AF XY: 0.503 AC XY: 37360 AN XY: 74314

African (AFR) AF: 0.433 AC: 17942 AN: 41454

American (AMR) AF: 0.482 AC: 7363 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.507 AC: 1759 AN: 3472

East Asian (EAS) AF: 0.262 AC: 1356 AN: 5174

South Asian (SAS) AF: 0.426 AC: 2059 AN: 4828

European-Finnish (FIN) AF: 0.511 AC: 5405 AN: 10568

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

European-Non Finnish (NFE) AF: 0.584 AC: 39683 AN: 67968

Other (OTH) AF: 0.494 AC: 1045 AN: 2114

Alfa AF: 0.541 Hom.: 4811

Bravo AF: 0.508

Asia WGS AF: 0.344 AC: 1199 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.39
DANN	Benign	0.49
PhyloP100		-1.4
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: rs1409071; hg19: chr13-21962773;