9-14654902-C-T

Variant names:

• chr9-14654902-C-T
• rs7853156
• NM_178566.6:c.504+3847G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 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=-0.73).
• 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 rank	MANE	Protein	UniProt
ZDHHC21	NM_178566.6	c.504+3847G>A		intron_variant	Intron 7 of 9	ENST00000380916.9	NP_848661.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZDHHC21	ENST00000380916.9	c.504+3847G>A		intron_variant	Intron 7 of 9	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

African (AFR) AF: 0.0927 AC: 3843 AN: 41468

American (AMR) AF: 0.123 AC: 1873 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.190 AC: 659 AN: 3468

East Asian (EAS) AF: 0.311 AC: 1602 AN: 5150

South Asian (SAS) AF: 0.342 AC: 1645 AN: 4804

European-Finnish (FIN) AF: 0.193 AC: 2035 AN: 10556

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.170 AC: 11546 AN: 67822

Other (OTH) AF: 0.153 AC: 323 AN: 2108

Alfa AF: 0.167 Hom.: 1841

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
PhyloP100		-0.047
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: rs7853156; hg19: chr9-14654900;