chr9-14678732-T-C

Variant names:

• chr9-14678732-T-C
• rs9298706
• NM_178566.6:c.-46+1301A>G

Variant summary

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

The NM_178566.6(ZDHHC21):​c.-46+1301A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.253 in 151,984 control chromosomes in the GnomAD database, including 5,392 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 0.25 (5392 hom., cov: 32)
• Consequence: ZDHHC21 NM_178566.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0650
• Publications: 6 publications found

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

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.359 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZDHHC21	NM_178566.6	c.-46+1301A>G		intron_variant	Intron 3 of 9	ENST00000380916.9	NP_848661.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZDHHC21	ENST00000380916.9	c.-46+1301A>G		intron_variant	Intron 3 of 9	1	NM_178566.6	ENSP00000370303.3

Frequencies

GnomAD3 genomes AF: 0.254 AC: 38520 AN: 151866 Hom.: 5393 Cov.: 32

Gnomad AFR AF: 0.139

Gnomad AMI AF: 0.195

Gnomad AMR AF: 0.268

Gnomad ASJ AF: 0.278

Gnomad EAS AF: 0.373

Gnomad SAS AF: 0.180

Gnomad FIN AF: 0.264

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.314

Gnomad OTH AF: 0.262

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

GnomAD4 genome AF: 0.253 AC: 38521 AN: 151984 Hom.: 5392 Cov.: 32 AF XY: 0.252 AC XY: 18690 AN XY: 74270

African (AFR) AF: 0.139 AC: 5767 AN: 41500

American (AMR) AF: 0.267 AC: 4076 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.278 AC: 964 AN: 3468

East Asian (EAS) AF: 0.373 AC: 1929 AN: 5170

South Asian (SAS) AF: 0.178 AC: 861 AN: 4830

European-Finnish (FIN) AF: 0.264 AC: 2793 AN: 10572

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.314 AC: 21334 AN: 67896

Other (OTH) AF: 0.258 AC: 543 AN: 2106

Alfa AF: 0.279 Hom.: 1781

Bravo AF: 0.252

Asia WGS AF: 0.227 AC: 789 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.2
DANN	Benign	0.58
PhyloP100		0.065
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: rs9298706; hg19: chr9-14678730; COSMIC: COSV66612814;