9-14654902-C-T

Position:

• chr9-14654902-C-T

Variant summary

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

The NM_178566.6(ZDHHC21):​c.504+3847G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.156 in 151,818 control chromosomes in the GnomAD database, including 2,098 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 0.16 (2098 hom., cov: 32)
• Consequence: ZDHHC21 NM_178566.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0470

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=-0.73).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.329 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZDHHC21	NM_178566.6	c.504+3847G>A		intron_variant		ENST00000380916.9	NP_848661.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZDHHC21	ENST00000380916.9	c.504+3847G>A		intron_variant		1	NM_178566.6	ENSP00000370303.3

Frequencies

GnomAD3 genomes AF: 0.156 AC: 23664 AN: 151700 Hom.: 2096 Cov.: 32

Gnomad AFR AF: 0.0929

Gnomad AMI AF: 0.108

Gnomad AMR AF: 0.123

Gnomad ASJ AF: 0.190

Gnomad EAS AF: 0.311

Gnomad SAS AF: 0.342

Gnomad FIN AF: 0.193

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.153

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

GnomAD4 genome AF: 0.156 AC: 23673 AN: 151818 Hom.: 2098 Cov.: 32 AF XY: 0.159 AC XY: 11776 AN XY: 74176

Gnomad4 AFR AF: 0.0927

Gnomad4 AMR AF: 0.123

Gnomad4 ASJ AF: 0.190

Gnomad4 EAS AF: 0.311

Gnomad4 SAS AF: 0.342

Gnomad4 FIN AF: 0.193

Gnomad4 NFE AF: 0.170

Gnomad4 OTH AF: 0.153

Alfa AF: 0.162 Hom.: 1238

Bravo AF: 0.144

Asia WGS AF: 0.278 AC: 966 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	5.8
DANN	Benign	0.86

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: rs7853156; hg19: chr9-14654900;