rs1409071

chr13-21388634-A-G

Variant summary

Our verdict is Benign. Variant got -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

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]

MIPEPP3 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
ZDHHC20	NM_001330059.2	c.728-1000T>C		intron_variant		ENST00000400590.8
MIPEPP3	NR_046461.1	n.571-3116A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZDHHC20	ENST00000400590.8	c.728-1000T>C		intron_variant		5	NM_001330059.2	P1

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

Gnomad4 AFR AF: 0.433

Gnomad4 AMR AF: 0.482

Gnomad4 ASJ AF: 0.507

Gnomad4 EAS AF: 0.262

Gnomad4 SAS AF: 0.426

Gnomad4 FIN AF: 0.511

Gnomad4 NFE AF: 0.584

Gnomad4 OTH AF: 0.494

Alfa AF: 0.544 Hom.: 4739

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

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

Publications

LitVar

Other links and lift over

dbSNP: rs1409071; hg19: chr13-21962773;