rs10481503

chr9-14660702-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_178566.6(ZDHHC21):c.365+1513C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.244 in 151,842 control chromosomes in the GnomAD database, including 5,071 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 0.24 (5071 hom., cov: 31)
• Consequence: ZDHHC21 NM_178566.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.372

Genes affected

ZDHHC21 (HGNC:20750): (zinc finger DHHC-type palmitoyltransferase 21) Enables palmitoyltransferase activity. Involved in peptidyl-L-cysteine S-palmitoylation. Located in Golgi apparatus and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.6).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.337 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZDHHC21	NM_178566.6	c.365+1513C>T		intron_variant		ENST00000380916.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZDHHC21	ENST00000380916.9	c.365+1513C>T		intron_variant		1	NM_178566.6	P1

Frequencies

GnomAD3 genomes AF: 0.245 AC: 37121 AN: 151724 Hom.: 5076 Cov.: 31

Gnomad AFR AF: 0.126

Gnomad AMI AF: 0.195

Gnomad AMR AF: 0.250

Gnomad ASJ AF: 0.275

Gnomad EAS AF: 0.350

Gnomad SAS AF: 0.183

Gnomad FIN AF: 0.251

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.309

Gnomad OTH AF: 0.256

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

GnomAD4 genome AF: 0.244 AC: 37111 AN: 151842 Hom.: 5071 Cov.: 31 AF XY: 0.242 AC XY: 17951 AN XY: 74194

Gnomad4 AFR AF: 0.126

Gnomad4 AMR AF: 0.250

Gnomad4 ASJ AF: 0.275

Gnomad4 EAS AF: 0.350

Gnomad4 SAS AF: 0.182

Gnomad4 FIN AF: 0.251

Gnomad4 NFE AF: 0.309

Gnomad4 OTH AF: 0.252

Alfa AF: 0.297 Hom.: 10537

Bravo AF: 0.242

Asia WGS AF: 0.216 AC: 752 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
Cadd	Benign	11
Dann	Benign	0.84

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: rs10481503; hg19: chr9-14660700; COSMIC: COSV66612742;